Introduction

This report outlines the initial bioinformatic steps performed to process the raw data for the Single cell RNA sequencing of vascular smooth muscle cells from atherosclerotic lesions of ApoE ko mice study [https://www.ncbi.nlm.nih.gov/bioproject/626450]. It covers:

Downloading the raw sequencing reads (FASTQ files).
Preparing the reference transcriptome.
Building the Salmon index required for quantification.
Running Salmon to quantify transcript abundances for each cell/sample.

The output of this stage is typically a set of quantification files (e.g., quant.sf) per sample, which are then further processed to generate a count matrix (often represented as a SingleCellExperiment object, as detailed in subsequent reports).

1. Raw Data Acquisition

The raw sequencing data (FASTQ files) were obtained from Sequence Read Archive (SRA) database with Accession Number PRJNA626450.


wget -c -O SMC-152_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/018/SRR11573318/SRR11573318.fastq.gz
wget -c -O SMC-152_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/009/SRR11592409/SRR11592409.fastq.gz
wget -c -O SMC-153_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/017/SRR11573317/SRR11573317.fastq.gz
wget -c -O SMC-153_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/008/SRR11592408/SRR11592408.fastq.gz
wget -c -O SMC-154_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/016/SRR11573316/SRR11573316.fastq.gz
wget -c -O SMC-154_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/007/SRR11592407/SRR11592407.fastq.gz
wget -c -O SMC-155_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/015/SRR11573315/SRR11573315.fastq.gz
wget -c -O SMC-155_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/006/SRR11592406/SRR11592406.fastq.gz
wget -c -O SMC-156_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/014/SRR11573314/SRR11573314.fastq.gz
wget -c -O SMC-156_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/005/SRR11592405/SRR11592405.fastq.gz
wget -c -O SMC-157_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/013/SRR11573313/SRR11573313.fastq.gz
wget -c -O SMC-157_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/004/SRR11592404/SRR11592404.fastq.gz
wget -c -O SMC-158_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/012/SRR11573312/SRR11573312.fastq.gz
wget -c -O SMC-158_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/003/SRR11592403/SRR11592403.fastq.gz
wget -c -O SMC-159_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/011/SRR11573311/SRR11573311.fastq.gz
wget -c -O SMC-159_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/002/SRR11592402/SRR11592402.fastq.gz
wget -c -O SMC-160_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/010/SRR11573310/SRR11573310.fastq.gz
wget -c -O SMC-160_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/001/SRR11592401/SRR11592401.fastq.gz
wget -c -O SMC-100_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/074/SRR11573374/SRR11573374.fastq.gz
wget -c -O SMC-100_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/033/SRR11592433/SRR11592433.fastq.gz
wget -c -O SMC-102_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/073/SRR11573373/SRR11573373.fastq.gz
wget -c -O SMC-102_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/023/SRR11592523/SRR11592523.fastq.gz
wget -c -O SMC-103_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/072/SRR11573372/SRR11573372.fastq.gz
wget -c -O SMC-103_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/022/SRR11592522/SRR11592522.fastq.gz
wget -c -O SMC-104_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/071/SRR11573371/SRR11573371.fastq.gz
wget -c -O SMC-104_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/021/SRR11592521/SRR11592521.fastq.gz
wget -c -O SMC-105_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/070/SRR11573370/SRR11573370.fastq.gz
wget -c -O SMC-105_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/020/SRR11592520/SRR11592520.fastq.gz
wget -c -O SMC-106_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/069/SRR11573369/SRR11573369.fastq.gz
wget -c -O SMC-106_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/019/SRR11592519/SRR11592519.fastq.gz
wget -c -O SMC-107_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/068/SRR11573368/SRR11573368.fastq.gz
wget -c -O SMC-107_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/018/SRR11592518/SRR11592518.fastq.gz
wget -c -O SMC-108_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/067/SRR11573367/SRR11573367.fastq.gz
wget -c -O SMC-108_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/017/SRR11592517/SRR11592517.fastq.gz
wget -c -O SMC-109_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/066/SRR11573366/SRR11573366.fastq.gz
wget -c -O SMC-109_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/016/SRR11592516/SRR11592516.fastq.gz
wget -c -O SMC-110_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/065/SRR11573365/SRR11573365.fastq.gz
wget -c -O SMC-110_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/015/SRR11592515/SRR11592515.fastq.gz
wget -c -O SMC-111_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/063/SRR11573363/SRR11573363.fastq.gz
wget -c -O SMC-111_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/013/SRR11592513/SRR11592513.fastq.gz
wget -c -O SMC-112_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/062/SRR11573362/SRR11573362.fastq.gz
wget -c -O SMC-112_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/012/SRR11592512/SRR11592512.fastq.gz
wget -c -O SMC-113_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/061/SRR11573361/SRR11573361.fastq.gz
wget -c -O SMC-113_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/011/SRR11592511/SRR11592511.fastq.gz
wget -c -O SMC-114_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/060/SRR11573360/SRR11573360.fastq.gz
wget -c -O SMC-114_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/010/SRR11592510/SRR11592510.fastq.gz
wget -c -O SMC-115_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/059/SRR11573359/SRR11573359.fastq.gz
wget -c -O SMC-115_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/009/SRR11592509/SRR11592509.fastq.gz
wget -c -O SMC-116_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/058/SRR11573358/SRR11573358.fastq.gz
wget -c -O SMC-116_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/008/SRR11592508/SRR11592508.fastq.gz
wget -c -O SMC-117_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/057/SRR11573357/SRR11573357.fastq.gz
wget -c -O SMC-117_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/007/SRR11592507/SRR11592507.fastq.gz
wget -c -O SMC-118_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/056/SRR11573356/SRR11573356.fastq.gz
wget -c -O SMC-118_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/006/SRR11592506/SRR11592506.fastq.gz
wget -c -O SMC-119_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/055/SRR11573355/SRR11573355.fastq.gz
wget -c -O SMC-119_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/005/SRR11592505/SRR11592505.fastq.gz
wget -c -O SMC-12_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/064/SRR11573364/SRR11573364.fastq.gz
wget -c -O SMC-12_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/014/SRR11592514/SRR11592514.fastq.gz
wget -c -O SMC-120_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/054/SRR11573354/SRR11573354.fastq.gz
wget -c -O SMC-120_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/004/SRR11592504/SRR11592504.fastq.gz
wget -c -O SMC-121_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/052/SRR11573352/SRR11573352.fastq.gz
wget -c -O SMC-121_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/002/SRR11592502/SRR11592502.fastq.gz
wget -c -O SMC-122_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/051/SRR11573351/SRR11573351.fastq.gz
wget -c -O SMC-122_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/001/SRR11592501/SRR11592501.fastq.gz
wget -c -O SMC-123_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/050/SRR11573350/SRR11573350.fastq.gz
wget -c -O SMC-123_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/000/SRR11592500/SRR11592500.fastq.gz
wget -c -O SMC-124_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/049/SRR11573349/SRR11573349.fastq.gz
wget -c -O SMC-124_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/099/SRR11592499/SRR11592499.fastq.gz
wget -c -O SMC-125_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/048/SRR11573348/SRR11573348.fastq.gz
wget -c -O SMC-125_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/098/SRR11592498/SRR11592498.fastq.gz
wget -c -O SMC-126_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/047/SRR11573347/SRR11573347.fastq.gz
wget -c -O SMC-126_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/097/SRR11592497/SRR11592497.fastq.gz
wget -c -O SMC-127_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/046/SRR11573346/SRR11573346.fastq.gz
wget -c -O SMC-127_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/096/SRR11592496/SRR11592496.fastq.gz
wget -c -O SMC-128_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/045/SRR11573345/SRR11573345.fastq.gz
wget -c -O SMC-128_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/095/SRR11592495/SRR11592495.fastq.gz
wget -c -O SMC-129_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/044/SRR11573344/SRR11573344.fastq.gz
wget -c -O SMC-129_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/094/SRR11592494/SRR11592494.fastq.gz
wget -c -O SMC-13_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/053/SRR11573353/SRR11573353.fastq.gz
wget -c -O SMC-13_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/003/SRR11592503/SRR11592503.fastq.gz
wget -c -O SMC-130_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/043/SRR11573343/SRR11573343.fastq.gz
wget -c -O SMC-130_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/093/SRR11592493/SRR11592493.fastq.gz
wget -c -O SMC-131_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/041/SRR11573341/SRR11573341.fastq.gz
wget -c -O SMC-131_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/032/SRR11592432/SRR11592432.fastq.gz
wget -c -O SMC-132_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/040/SRR11573340/SRR11573340.fastq.gz
wget -c -O SMC-132_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/031/SRR11592431/SRR11592431.fastq.gz
wget -c -O SMC-133_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/039/SRR11573339/SRR11573339.fastq.gz
wget -c -O SMC-133_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/030/SRR11592430/SRR11592430.fastq.gz
wget -c -O SMC-134_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/038/SRR11573338/SRR11573338.fastq.gz
wget -c -O SMC-134_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/029/SRR11592429/SRR11592429.fastq.gz
wget -c -O SMC-135_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/037/SRR11573337/SRR11573337.fastq.gz
wget -c -O SMC-135_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/028/SRR11592428/SRR11592428.fastq.gz
wget -c -O SMC-136_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/036/SRR11573336/SRR11573336.fastq.gz
wget -c -O SMC-136_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/027/SRR11592427/SRR11592427.fastq.gz
wget -c -O SMC-137_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/035/SRR11573335/SRR11573335.fastq.gz
wget -c -O SMC-137_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/026/SRR11592426/SRR11592426.fastq.gz
wget -c -O SMC-138_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/034/SRR11573334/SRR11573334.fastq.gz
wget -c -O SMC-138_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/025/SRR11592425/SRR11592425.fastq.gz
wget -c -O SMC-139_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/033/SRR11573333/SRR11573333.fastq.gz
wget -c -O SMC-139_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/024/SRR11592424/SRR11592424.fastq.gz
wget -c -O SMC-14_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/042/SRR11573342/SRR11573342.fastq.gz
wget -c -O SMC-14_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/092/SRR11592492/SRR11592492.fastq.gz
wget -c -O SMC-140_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/032/SRR11573332/SRR11573332.fastq.gz
wget -c -O SMC-140_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/023/SRR11592423/SRR11592423.fastq.gz
wget -c -O SMC-141_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/030/SRR11573330/SRR11573330.fastq.gz
wget -c -O SMC-141_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/021/SRR11592421/SRR11592421.fastq.gz
wget -c -O SMC-142_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/029/SRR11573329/SRR11573329.fastq.gz
wget -c -O SMC-142_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/020/SRR11592420/SRR11592420.fastq.gz
wget -c -O SMC-143_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/028/SRR11573328/SRR11573328.fastq.gz
wget -c -O SMC-143_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/019/SRR11592419/SRR11592419.fastq.gz
wget -c -O SMC-144_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/027/SRR11573327/SRR11573327.fastq.gz
wget -c -O SMC-144_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/018/SRR11592418/SRR11592418.fastq.gz
wget -c -O SMC-145_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/026/SRR11573326/SRR11573326.fastq.gz
wget -c -O SMC-145_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/017/SRR11592417/SRR11592417.fastq.gz
wget -c -O SMC-146_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/025/SRR11573325/SRR11573325.fastq.gz
wget -c -O SMC-146_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/016/SRR11592416/SRR11592416.fastq.gz
wget -c -O SMC-147_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/024/SRR11573324/SRR11573324.fastq.gz
wget -c -O SMC-147_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/015/SRR11592415/SRR11592415.fastq.gz
wget -c -O SMC-148_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/023/SRR11573323/SRR11573323.fastq.gz
wget -c -O SMC-148_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/014/SRR11592414/SRR11592414.fastq.gz
wget -c -O SMC-149_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/022/SRR11573322/SRR11573322.fastq.gz
wget -c -O SMC-149_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/013/SRR11592413/SRR11592413.fastq.gz
wget -c -O SMC-15_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/031/SRR11573331/SRR11573331.fastq.gz
wget -c -O SMC-15_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/022/SRR11592422/SRR11592422.fastq.gz
wget -c -O SMC-150_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/021/SRR11573321/SRR11573321.fastq.gz
wget -c -O SMC-150_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/012/SRR11592412/SRR11592412.fastq.gz
wget -c -O SMC-151_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/019/SRR11573319/SRR11573319.fastq.gz
wget -c -O SMC-151_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/010/SRR11592410/SRR11592410.fastq.gz
wget -c -O SMC-16_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/020/SRR11573320/SRR11573320.fastq.gz
wget -c -O SMC-16_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/011/SRR11592411/SRR11592411.fastq.gz
wget -c -O SMC-96_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/078/SRR11573378/SRR11573378.fastq.gz
wget -c -O SMC-96_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/037/SRR11592437/SRR11592437.fastq.gz
wget -c -O SMC-97_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/077/SRR11573377/SRR11573377.fastq.gz
wget -c -O SMC-97_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/036/SRR11592436/SRR11592436.fastq.gz
wget -c -O SMC-98_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/076/SRR11573376/SRR11573376.fastq.gz
wget -c -O SMC-98_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/035/SRR11592435/SRR11592435.fastq.gz
wget -c -O SMC-99_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/075/SRR11573375/SRR11573375.fastq.gz
wget -c -O SMC-99_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/034/SRR11592434/SRR11592434.fastq.gz
wget -c -O SMC-10_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/084/SRR11573384/SRR11573384.fastq.gz
wget -c -O SMC-10_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/043/SRR11592443/SRR11592443.fastq.gz
wget -c -O SMC-60_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/018/SRR11573418/SRR11573418.fastq.gz
wget -c -O SMC-60_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/041/SRR11592541/SRR11592541.fastq.gz
wget -c -O SMC-61_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/016/SRR11573416/SRR11573416.fastq.gz
wget -c -O SMC-61_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/039/SRR11592539/SRR11592539.fastq.gz
wget -c -O SMC-62_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/015/SRR11573415/SRR11573415.fastq.gz
wget -c -O SMC-62_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/038/SRR11592538/SRR11592538.fastq.gz
wget -c -O SMC-63_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/014/SRR11573414/SRR11573414.fastq.gz
wget -c -O SMC-63_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/037/SRR11592537/SRR11592537.fastq.gz
wget -c -O SMC-64_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/013/SRR11573413/SRR11573413.fastq.gz
wget -c -O SMC-64_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/036/SRR11592536/SRR11592536.fastq.gz
wget -c -O SMC-65_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/012/SRR11573412/SRR11573412.fastq.gz
wget -c -O SMC-65_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/035/SRR11592535/SRR11592535.fastq.gz
wget -c -O SMC-66_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/011/SRR11573411/SRR11573411.fastq.gz
wget -c -O SMC-66_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/034/SRR11592534/SRR11592534.fastq.gz
wget -c -O SMC-67_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/010/SRR11573410/SRR11573410.fastq.gz
wget -c -O SMC-67_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/033/SRR11592533/SRR11592533.fastq.gz
wget -c -O SMC-68_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/009/SRR11573409/SRR11573409.fastq.gz
wget -c -O SMC-68_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/032/SRR11592532/SRR11592532.fastq.gz
wget -c -O SMC-69_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/008/SRR11573408/SRR11573408.fastq.gz
wget -c -O SMC-69_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/031/SRR11592531/SRR11592531.fastq.gz
wget -c -O SMC-7_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/017/SRR11573417/SRR11573417.fastq.gz
wget -c -O SMC-7_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/040/SRR11592540/SRR11592540.fastq.gz
wget -c -O SMC-70_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/007/SRR11573407/SRR11573407.fastq.gz
wget -c -O SMC-70_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/030/SRR11592530/SRR11592530.fastq.gz
wget -c -O SMC-71_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/005/SRR11573405/SRR11573405.fastq.gz
wget -c -O SMC-71_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/028/SRR11592528/SRR11592528.fastq.gz
wget -c -O SMC-72_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/004/SRR11573404/SRR11573404.fastq.gz
wget -c -O SMC-72_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/027/SRR11592527/SRR11592527.fastq.gz
wget -c -O SMC-73_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/003/SRR11573403/SRR11573403.fastq.gz
wget -c -O SMC-73_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/026/SRR11592526/SRR11592526.fastq.gz
wget -c -O SMC-74_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/002/SRR11573402/SRR11573402.fastq.gz
wget -c -O SMC-74_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/025/SRR11592525/SRR11592525.fastq.gz
wget -c -O SMC-75_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/001/SRR11573401/SRR11573401.fastq.gz
wget -c -O SMC-75_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/024/SRR11592524/SRR11592524.fastq.gz
wget -c -O SMC-76_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/000/SRR11573400/SRR11573400.fastq.gz
wget -c -O SMC-76_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/059/SRR11592459/SRR11592459.fastq.gz
wget -c -O SMC-77_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/099/SRR11573399/SRR11573399.fastq.gz
wget -c -O SMC-77_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/058/SRR11592458/SRR11592458.fastq.gz
wget -c -O SMC-78_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/098/SRR11573398/SRR11573398.fastq.gz
wget -c -O SMC-78_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/057/SRR11592457/SRR11592457.fastq.gz
wget -c -O SMC-79_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/097/SRR11573397/SRR11573397.fastq.gz
wget -c -O SMC-79_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/056/SRR11592456/SRR11592456.fastq.gz
wget -c -O SMC-8_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/006/SRR11573406/SRR11573406.fastq.gz
wget -c -O SMC-8_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/029/SRR11592529/SRR11592529.fastq.gz
wget -c -O SMC-80_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/096/SRR11573396/SRR11573396.fastq.gz
wget -c -O SMC-80_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/055/SRR11592455/SRR11592455.fastq.gz
wget -c -O SMC-81_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/094/SRR11573394/SRR11573394.fastq.gz
wget -c -O SMC-81_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/053/SRR11592453/SRR11592453.fastq.gz
wget -c -O SMC-82_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/093/SRR11573393/SRR11573393.fastq.gz
wget -c -O SMC-82_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/052/SRR11592452/SRR11592452.fastq.gz
wget -c -O SMC-83_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/092/SRR11573392/SRR11573392.fastq.gz
wget -c -O SMC-83_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/051/SRR11592451/SRR11592451.fastq.gz
wget -c -O SMC-84_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/091/SRR11573391/SRR11573391.fastq.gz
wget -c -O SMC-84_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/050/SRR11592450/SRR11592450.fastq.gz
wget -c -O SMC-85_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/090/SRR11573390/SRR11573390.fastq.gz
wget -c -O SMC-85_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/049/SRR11592449/SRR11592449.fastq.gz
wget -c -O SMC-86_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/089/SRR11573389/SRR11573389.fastq.gz
wget -c -O SMC-86_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/048/SRR11592448/SRR11592448.fastq.gz
wget -c -O SMC-87_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/088/SRR11573388/SRR11573388.fastq.gz
wget -c -O SMC-87_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/047/SRR11592447/SRR11592447.fastq.gz
wget -c -O SMC-88_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/087/SRR11573387/SRR11573387.fastq.gz
wget -c -O SMC-88_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/046/SRR11592446/SRR11592446.fastq.gz
wget -c -O SMC-89_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/086/SRR11573386/SRR11573386.fastq.gz
wget -c -O SMC-89_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/045/SRR11592445/SRR11592445.fastq.gz
wget -c -O SMC-9_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/095/SRR11573395/SRR11573395.fastq.gz
wget -c -O SMC-9_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/054/SRR11592454/SRR11592454.fastq.gz
wget -c -O SMC-90_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/085/SRR11573385/SRR11573385.fastq.gz
wget -c -O SMC-90_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/044/SRR11592444/SRR11592444.fastq.gz
wget -c -O SMC-91_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/083/SRR11573383/SRR11573383.fastq.gz
wget -c -O SMC-91_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/042/SRR11592442/SRR11592442.fastq.gz
wget -c -O SMC-92_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/082/SRR11573382/SRR11573382.fastq.gz
wget -c -O SMC-92_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/041/SRR11592441/SRR11592441.fastq.gz
wget -c -O SMC-93_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/081/SRR11573381/SRR11573381.fastq.gz
wget -c -O SMC-93_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/040/SRR11592440/SRR11592440.fastq.gz
wget -c -O SMC-94_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/080/SRR11573380/SRR11573380.fastq.gz
wget -c -O SMC-94_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/039/SRR11592439/SRR11592439.fastq.gz
wget -c -O SMC-95_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/079/SRR11573379/SRR11573379.fastq.gz
wget -c -O SMC-95_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/038/SRR11592438/SRR11592438.fastq.gz
wget -c -O SMC-177_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/078/SRR11573478/SRR11573478.fastq.gz
wget -c -O SMC-177_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/069/SRR11592569/SRR11592569.fastq.gz
wget -c -O SMC-178_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/077/SRR11573477/SRR11573477.fastq.gz
wget -c -O SMC-178_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/068/SRR11592568/SRR11592568.fastq.gz
wget -c -O SMC-179_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/076/SRR11573476/SRR11573476.fastq.gz
wget -c -O SMC-179_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/067/SRR11592567/SRR11592567.fastq.gz
wget -c -O SMC-180_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/075/SRR11573475/SRR11573475.fastq.gz
wget -c -O SMC-180_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/066/SRR11592566/SRR11592566.fastq.gz
wget -c -O SMC-181_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/073/SRR11573473/SRR11573473.fastq.gz
wget -c -O SMC-181_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/064/SRR11592564/SRR11592564.fastq.gz
wget -c -O SMC-182_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/072/SRR11573472/SRR11573472.fastq.gz
wget -c -O SMC-182_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/063/SRR11592563/SRR11592563.fastq.gz
wget -c -O SMC-183_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/071/SRR11573471/SRR11573471.fastq.gz
wget -c -O SMC-183_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/062/SRR11592562/SRR11592562.fastq.gz
wget -c -O SMC-184_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/070/SRR11573470/SRR11573470.fastq.gz
wget -c -O SMC-184_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/061/SRR11592561/SRR11592561.fastq.gz
wget -c -O SMC-185_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/069/SRR11573469/SRR11573469.fastq.gz
wget -c -O SMC-185_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/060/SRR11592560/SRR11592560.fastq.gz
wget -c -O SMC-186_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/068/SRR11573468/SRR11573468.fastq.gz
wget -c -O SMC-186_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/059/SRR11592559/SRR11592559.fastq.gz
wget -c -O SMC-187_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/067/SRR11573467/SRR11573467.fastq.gz
wget -c -O SMC-187_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/058/SRR11592558/SRR11592558.fastq.gz
wget -c -O SMC-188_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/066/SRR11573466/SRR11573466.fastq.gz
wget -c -O SMC-188_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/057/SRR11592557/SRR11592557.fastq.gz
wget -c -O SMC-189_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/065/SRR11573465/SRR11573465.fastq.gz
wget -c -O SMC-189_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/056/SRR11592556/SRR11592556.fastq.gz
wget -c -O SMC-19_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/074/SRR11573474/SRR11573474.fastq.gz
wget -c -O SMC-19_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/065/SRR11592565/SRR11592565.fastq.gz
wget -c -O SMC-190_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/064/SRR11573464/SRR11573464.fastq.gz
wget -c -O SMC-190_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/091/SRR11592491/SRR11592491.fastq.gz
wget -c -O SMC-191_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/062/SRR11573462/SRR11573462.fastq.gz
wget -c -O SMC-191_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/089/SRR11592489/SRR11592489.fastq.gz
wget -c -O SMC-20_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/063/SRR11573463/SRR11573463.fastq.gz
wget -c -O SMC-20_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/090/SRR11592490/SRR11592490.fastq.gz
wget -c -O SMC-21_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/060/SRR11573460/SRR11573460.fastq.gz
wget -c -O SMC-21_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/087/SRR11592487/SRR11592487.fastq.gz
wget -c -O SMC-22_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/059/SRR11573459/SRR11573459.fastq.gz
wget -c -O SMC-22_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/086/SRR11592486/SRR11592486.fastq.gz
wget -c -O SMC-23_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/058/SRR11573458/SRR11573458.fastq.gz
wget -c -O SMC-23_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/085/SRR11592485/SRR11592485.fastq.gz
wget -c -O SMC-24_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/057/SRR11573457/SRR11573457.fastq.gz
wget -c -O SMC-24_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/084/SRR11592484/SRR11592484.fastq.gz
wget -c -O SMC-25_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/056/SRR11573456/SRR11573456.fastq.gz
wget -c -O SMC-25_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/083/SRR11592483/SRR11592483.fastq.gz
wget -c -O SMC-26_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/055/SRR11573455/SRR11573455.fastq.gz
wget -c -O SMC-26_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/082/SRR11592482/SRR11592482.fastq.gz
wget -c -O SMC-27_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/054/SRR11573454/SRR11573454.fastq.gz
wget -c -O SMC-27_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/081/SRR11592481/SRR11592481.fastq.gz
wget -c -O SMC-28_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/053/SRR11573453/SRR11573453.fastq.gz
wget -c -O SMC-28_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/080/SRR11592480/SRR11592480.fastq.gz
wget -c -O SMC-29_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/052/SRR11573452/SRR11573452.fastq.gz
wget -c -O SMC-29_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/079/SRR11592479/SRR11592479.fastq.gz
wget -c -O SMC-3_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/061/SRR11573461/SRR11573461.fastq.gz
wget -c -O SMC-3_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/088/SRR11592488/SRR11592488.fastq.gz
wget -c -O SMC-30_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/051/SRR11573451/SRR11573451.fastq.gz
wget -c -O SMC-30_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/078/SRR11592478/SRR11592478.fastq.gz
wget -c -O SMC-31_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/049/SRR11573449/SRR11573449.fastq.gz
wget -c -O SMC-31_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/076/SRR11592476/SRR11592476.fastq.gz
wget -c -O SMC-32_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/048/SRR11573448/SRR11573448.fastq.gz
wget -c -O SMC-32_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/075/SRR11592475/SRR11592475.fastq.gz
wget -c -O SMC-33_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/047/SRR11573447/SRR11573447.fastq.gz
wget -c -O SMC-33_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/074/SRR11592474/SRR11592474.fastq.gz
wget -c -O SMC-34_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/046/SRR11573446/SRR11573446.fastq.gz
wget -c -O SMC-34_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/073/SRR11592473/SRR11592473.fastq.gz
wget -c -O SMC-35_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/045/SRR11573445/SRR11573445.fastq.gz
wget -c -O SMC-35_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/072/SRR11592472/SRR11592472.fastq.gz
wget -c -O SMC-36_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/044/SRR11573444/SRR11573444.fastq.gz
wget -c -O SMC-36_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/071/SRR11592471/SRR11592471.fastq.gz
wget -c -O SMC-37_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/043/SRR11573443/SRR11573443.fastq.gz
wget -c -O SMC-37_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/070/SRR11592470/SRR11592470.fastq.gz
wget -c -O SMC-38_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/042/SRR11573442/SRR11573442.fastq.gz
wget -c -O SMC-38_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/069/SRR11592469/SRR11592469.fastq.gz
wget -c -O SMC-39_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/041/SRR11573441/SRR11573441.fastq.gz
wget -c -O SMC-39_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/068/SRR11592468/SRR11592468.fastq.gz
wget -c -O SMC-4_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/050/SRR11573450/SRR11573450.fastq.gz
wget -c -O SMC-4_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/077/SRR11592477/SRR11592477.fastq.gz
wget -c -O SMC-40_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/040/SRR11573440/SRR11573440.fastq.gz
wget -c -O SMC-40_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/067/SRR11592467/SRR11592467.fastq.gz
wget -c -O SMC-41_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/038/SRR11573438/SRR11573438.fastq.gz
wget -c -O SMC-41_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/065/SRR11592465/SRR11592465.fastq.gz
wget -c -O SMC-42_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/037/SRR11573437/SRR11573437.fastq.gz
wget -c -O SMC-42_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/064/SRR11592464/SRR11592464.fastq.gz
wget -c -O SMC-43_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/036/SRR11573436/SRR11573436.fastq.gz
wget -c -O SMC-43_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/063/SRR11592463/SRR11592463.fastq.gz
wget -c -O SMC-44_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/035/SRR11573435/SRR11573435.fastq.gz
wget -c -O SMC-44_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/062/SRR11592462/SRR11592462.fastq.gz
wget -c -O SMC-45_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/034/SRR11573434/SRR11573434.fastq.gz
wget -c -O SMC-45_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/061/SRR11592461/SRR11592461.fastq.gz
wget -c -O SMC-46_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/033/SRR11573433/SRR11573433.fastq.gz
wget -c -O SMC-46_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/060/SRR11592460/SRR11592460.fastq.gz
wget -c -O SMC-47_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/032/SRR11573432/SRR11573432.fastq.gz
wget -c -O SMC-47_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/055/SRR11592555/SRR11592555.fastq.gz
wget -c -O SMC-48_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/031/SRR11573431/SRR11573431.fastq.gz
wget -c -O SMC-48_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/054/SRR11592554/SRR11592554.fastq.gz
wget -c -O SMC-49_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/030/SRR11573430/SRR11573430.fastq.gz
wget -c -O SMC-49_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/053/SRR11592553/SRR11592553.fastq.gz
wget -c -O SMC-5_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/039/SRR11573439/SRR11573439.fastq.gz
wget -c -O SMC-5_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/066/SRR11592466/SRR11592466.fastq.gz
wget -c -O SMC-50_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/029/SRR11573429/SRR11573429.fastq.gz
wget -c -O SMC-50_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/052/SRR11592552/SRR11592552.fastq.gz
wget -c -O SMC-51_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/027/SRR11573427/SRR11573427.fastq.gz
wget -c -O SMC-51_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/050/SRR11592550/SRR11592550.fastq.gz
wget -c -O SMC-52_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/026/SRR11573426/SRR11573426.fastq.gz
wget -c -O SMC-52_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/049/SRR11592549/SRR11592549.fastq.gz
wget -c -O SMC-53_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/025/SRR11573425/SRR11573425.fastq.gz
wget -c -O SMC-53_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/048/SRR11592548/SRR11592548.fastq.gz
wget -c -O SMC-54_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/024/SRR11573424/SRR11573424.fastq.gz
wget -c -O SMC-54_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/047/SRR11592547/SRR11592547.fastq.gz
wget -c -O SMC-55_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/023/SRR11573423/SRR11573423.fastq.gz
wget -c -O SMC-55_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/046/SRR11592546/SRR11592546.fastq.gz
wget -c -O SMC-56_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/022/SRR11573422/SRR11573422.fastq.gz
wget -c -O SMC-56_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/045/SRR11592545/SRR11592545.fastq.gz
wget -c -O SMC-57_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/021/SRR11573421/SRR11573421.fastq.gz
wget -c -O SMC-57_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/044/SRR11592544/SRR11592544.fastq.gz
wget -c -O SMC-58_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/020/SRR11573420/SRR11573420.fastq.gz
wget -c -O SMC-58_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/043/SRR11592543/SRR11592543.fastq.gz
wget -c -O SMC-59_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/019/SRR11573419/SRR11573419.fastq.gz
wget -c -O SMC-59_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/042/SRR11592542/SRR11592542.fastq.gz
wget -c -O SMC-6_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/028/SRR11573428/SRR11573428.fastq.gz
wget -c -O SMC-6_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/051/SRR11592551/SRR11592551.fastq.gz
wget -c -O SMC-1_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/000/SRR11573500/SRR11573500.fastq.gz
wget -c -O SMC-1_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/091/SRR11592591/SRR11592591.fastq.gz
wget -c -O SMC-101_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/097/SRR11573497/SRR11573497.fastq.gz
wget -c -O SMC-101_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/088/SRR11592588/SRR11592588.fastq.gz
wget -c -O SMC-11_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/098/SRR11573498/SRR11573498.fastq.gz
wget -c -O SMC-11_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/089/SRR11592589/SRR11592589.fastq.gz
wget -c -O SMC-161_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/095/SRR11573495/SRR11573495.fastq.gz
wget -c -O SMC-161_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/086/SRR11592586/SRR11592586.fastq.gz
wget -c -O SMC-162_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/094/SRR11573494/SRR11573494.fastq.gz
wget -c -O SMC-162_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/085/SRR11592585/SRR11592585.fastq.gz
wget -c -O SMC-163_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/093/SRR11573493/SRR11573493.fastq.gz
wget -c -O SMC-163_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/084/SRR11592584/SRR11592584.fastq.gz
wget -c -O SMC-164_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/092/SRR11573492/SRR11573492.fastq.gz
wget -c -O SMC-164_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/083/SRR11592583/SRR11592583.fastq.gz
wget -c -O SMC-165_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/091/SRR11573491/SRR11573491.fastq.gz
wget -c -O SMC-165_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/082/SRR11592582/SRR11592582.fastq.gz
wget -c -O SMC-166_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/090/SRR11573490/SRR11573490.fastq.gz
wget -c -O SMC-166_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/081/SRR11592581/SRR11592581.fastq.gz
wget -c -O SMC-167_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/089/SRR11573489/SRR11573489.fastq.gz
wget -c -O SMC-167_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/080/SRR11592580/SRR11592580.fastq.gz
wget -c -O SMC-168_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/088/SRR11573488/SRR11573488.fastq.gz
wget -c -O SMC-168_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/079/SRR11592579/SRR11592579.fastq.gz
wget -c -O SMC-169_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/087/SRR11573487/SRR11573487.fastq.gz
wget -c -O SMC-169_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/078/SRR11592578/SRR11592578.fastq.gz
wget -c -O SMC-17_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/096/SRR11573496/SRR11573496.fastq.gz
wget -c -O SMC-17_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/087/SRR11592587/SRR11592587.fastq.gz
wget -c -O SMC-170_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/086/SRR11573486/SRR11573486.fastq.gz
wget -c -O SMC-170_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/077/SRR11592577/SRR11592577.fastq.gz
wget -c -O SMC-171_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/084/SRR11573484/SRR11573484.fastq.gz
wget -c -O SMC-171_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/075/SRR11592575/SRR11592575.fastq.gz
wget -c -O SMC-172_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/083/SRR11573483/SRR11573483.fastq.gz
wget -c -O SMC-172_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/074/SRR11592574/SRR11592574.fastq.gz
wget -c -O SMC-173_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/082/SRR11573482/SRR11573482.fastq.gz
wget -c -O SMC-173_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/073/SRR11592573/SRR11592573.fastq.gz
wget -c -O SMC-174_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/081/SRR11573481/SRR11573481.fastq.gz
wget -c -O SMC-174_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/072/SRR11592572/SRR11592572.fastq.gz
wget -c -O SMC-175_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/080/SRR11573480/SRR11573480.fastq.gz
wget -c -O SMC-175_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/071/SRR11592571/SRR11592571.fastq.gz
wget -c -O SMC-176_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/079/SRR11573479/SRR11573479.fastq.gz
wget -c -O SMC-176_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/070/SRR11592570/SRR11592570.fastq.gz
wget -c -O SMC-18_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/085/SRR11573485/SRR11573485.fastq.gz
wget -c -O SMC-18_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/076/SRR11592576/SRR11592576.fastq.gz
wget -c -O SMC-2_R1.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/099/SRR11573499/SRR11573499.fastq.gz
wget -c -O SMC-2_R2.fastq.gz ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/090/SRR11592590/SRR11592590.fastq.gz

2. Reference Transcriptome Preparation

A reference transcriptome is essential for quantifying gene expression. We used the reference from GENCODE (Release M36 (GRCm39)).

The following commands were used to download the necessary reference files.


mkdir -p index/mm_gencode_36

wget -c -O index/mm_gencode_36/genome.fa.gz ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M36/GRCm39.genome.fa.gz
wget -c -O index/mm_gencode_36/transcripts.fa.gz ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M36/gencode.vM36.transcripts.fa.gz

3. Building the Salmon Index

Salmon requires a specialized index built from the reference transcriptome. To improve quantification accuracy by accounting for reads mapping ambiguously outside annotated transcripts (common with pre-mRNA content or genomic contamination), decoy sequences representing the rest of the genome were included in the index.

The following Bash commands were used to build the Salmon index:


zcat index/mm_gencode_36/transcripts.fa.gz | grep "^>" | sed 's|[<>,]||g' >index/mm_gencode_36/transcripts.txt
gunzip -c index/mm_gencode_36/genome.fa.gz | grep "^>" | cut -d " " -f1 | sed 's/>//g' > "index/mm_gencode_36/decoys.txt"
cat index/mm_gencode_36/transcripts.fa.gz index/mm_gencode_36/genome.fa.gz >index/mm_gencode_36/gentrome.fa.gz

salmon index -t index/mm_gencode_36/gentrome.fa.gz -d index/mm_gencode_36/decoys.txt -p 8 -i index/mm_gencode_36 --gencode

4. Running Salmon Quantification

Salmon was used to quantify transcript abundance for each single-cell sample/library.

salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-152 -1 SMC-152_R1.fastq.gz -2 SMC-152_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-153 -1 SMC-153_R1.fastq.gz -2 SMC-153_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-154 -1 SMC-154_R1.fastq.gz -2 SMC-154_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-155 -1 SMC-155_R1.fastq.gz -2 SMC-155_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-156 -1 SMC-156_R1.fastq.gz -2 SMC-156_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-157 -1 SMC-157_R1.fastq.gz -2 SMC-157_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-158 -1 SMC-158_R1.fastq.gz -2 SMC-158_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-159 -1 SMC-159_R1.fastq.gz -2 SMC-159_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-160 -1 SMC-160_R1.fastq.gz -2 SMC-160_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-100 -1 SMC-100_R1.fastq.gz -2 SMC-100_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-102 -1 SMC-102_R1.fastq.gz -2 SMC-102_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-103 -1 SMC-103_R1.fastq.gz -2 SMC-103_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-104 -1 SMC-104_R1.fastq.gz -2 SMC-104_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-105 -1 SMC-105_R1.fastq.gz -2 SMC-105_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-106 -1 SMC-106_R1.fastq.gz -2 SMC-106_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-107 -1 SMC-107_R1.fastq.gz -2 SMC-107_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-108 -1 SMC-108_R1.fastq.gz -2 SMC-108_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-109 -1 SMC-109_R1.fastq.gz -2 SMC-109_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-110 -1 SMC-110_R1.fastq.gz -2 SMC-110_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-111 -1 SMC-111_R1.fastq.gz -2 SMC-111_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-112 -1 SMC-112_R1.fastq.gz -2 SMC-112_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-113 -1 SMC-113_R1.fastq.gz -2 SMC-113_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-114 -1 SMC-114_R1.fastq.gz -2 SMC-114_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-115 -1 SMC-115_R1.fastq.gz -2 SMC-115_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-116 -1 SMC-116_R1.fastq.gz -2 SMC-116_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-117 -1 SMC-117_R1.fastq.gz -2 SMC-117_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-118 -1 SMC-118_R1.fastq.gz -2 SMC-118_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-119 -1 SMC-119_R1.fastq.gz -2 SMC-119_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-12 -1 SMC-12_R1.fastq.gz -2 SMC-12_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-120 -1 SMC-120_R1.fastq.gz -2 SMC-120_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-121 -1 SMC-121_R1.fastq.gz -2 SMC-121_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-122 -1 SMC-122_R1.fastq.gz -2 SMC-122_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-123 -1 SMC-123_R1.fastq.gz -2 SMC-123_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-124 -1 SMC-124_R1.fastq.gz -2 SMC-124_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-125 -1 SMC-125_R1.fastq.gz -2 SMC-125_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-126 -1 SMC-126_R1.fastq.gz -2 SMC-126_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-127 -1 SMC-127_R1.fastq.gz -2 SMC-127_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-128 -1 SMC-128_R1.fastq.gz -2 SMC-128_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-129 -1 SMC-129_R1.fastq.gz -2 SMC-129_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-13 -1 SMC-13_R1.fastq.gz -2 SMC-13_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-130 -1 SMC-130_R1.fastq.gz -2 SMC-130_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-131 -1 SMC-131_R1.fastq.gz -2 SMC-131_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-132 -1 SMC-132_R1.fastq.gz -2 SMC-132_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-133 -1 SMC-133_R1.fastq.gz -2 SMC-133_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-134 -1 SMC-134_R1.fastq.gz -2 SMC-134_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-135 -1 SMC-135_R1.fastq.gz -2 SMC-135_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-136 -1 SMC-136_R1.fastq.gz -2 SMC-136_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-137 -1 SMC-137_R1.fastq.gz -2 SMC-137_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-138 -1 SMC-138_R1.fastq.gz -2 SMC-138_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-139 -1 SMC-139_R1.fastq.gz -2 SMC-139_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-14 -1 SMC-14_R1.fastq.gz -2 SMC-14_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-140 -1 SMC-140_R1.fastq.gz -2 SMC-140_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-141 -1 SMC-141_R1.fastq.gz -2 SMC-141_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-142 -1 SMC-142_R1.fastq.gz -2 SMC-142_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-143 -1 SMC-143_R1.fastq.gz -2 SMC-143_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-144 -1 SMC-144_R1.fastq.gz -2 SMC-144_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-145 -1 SMC-145_R1.fastq.gz -2 SMC-145_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-146 -1 SMC-146_R1.fastq.gz -2 SMC-146_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-147 -1 SMC-147_R1.fastq.gz -2 SMC-147_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-148 -1 SMC-148_R1.fastq.gz -2 SMC-148_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-149 -1 SMC-149_R1.fastq.gz -2 SMC-149_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-15 -1 SMC-15_R1.fastq.gz -2 SMC-15_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-150 -1 SMC-150_R1.fastq.gz -2 SMC-150_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-151 -1 SMC-151_R1.fastq.gz -2 SMC-151_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-16 -1 SMC-16_R1.fastq.gz -2 SMC-16_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-96 -1 SMC-96_R1.fastq.gz -2 SMC-96_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-97 -1 SMC-97_R1.fastq.gz -2 SMC-97_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-98 -1 SMC-98_R1.fastq.gz -2 SMC-98_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-99 -1 SMC-99_R1.fastq.gz -2 SMC-99_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-10 -1 SMC-10_R1.fastq.gz -2 SMC-10_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-60 -1 SMC-60_R1.fastq.gz -2 SMC-60_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-61 -1 SMC-61_R1.fastq.gz -2 SMC-61_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-62 -1 SMC-62_R1.fastq.gz -2 SMC-62_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-63 -1 SMC-63_R1.fastq.gz -2 SMC-63_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-64 -1 SMC-64_R1.fastq.gz -2 SMC-64_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-65 -1 SMC-65_R1.fastq.gz -2 SMC-65_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-66 -1 SMC-66_R1.fastq.gz -2 SMC-66_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-67 -1 SMC-67_R1.fastq.gz -2 SMC-67_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-68 -1 SMC-68_R1.fastq.gz -2 SMC-68_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-69 -1 SMC-69_R1.fastq.gz -2 SMC-69_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-7 -1 SMC-7_R1.fastq.gz -2 SMC-7_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-70 -1 SMC-70_R1.fastq.gz -2 SMC-70_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-71 -1 SMC-71_R1.fastq.gz -2 SMC-71_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-72 -1 SMC-72_R1.fastq.gz -2 SMC-72_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-73 -1 SMC-73_R1.fastq.gz -2 SMC-73_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-74 -1 SMC-74_R1.fastq.gz -2 SMC-74_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-75 -1 SMC-75_R1.fastq.gz -2 SMC-75_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-76 -1 SMC-76_R1.fastq.gz -2 SMC-76_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-77 -1 SMC-77_R1.fastq.gz -2 SMC-77_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-78 -1 SMC-78_R1.fastq.gz -2 SMC-78_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-79 -1 SMC-79_R1.fastq.gz -2 SMC-79_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-8 -1 SMC-8_R1.fastq.gz -2 SMC-8_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-80 -1 SMC-80_R1.fastq.gz -2 SMC-80_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-81 -1 SMC-81_R1.fastq.gz -2 SMC-81_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-82 -1 SMC-82_R1.fastq.gz -2 SMC-82_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-83 -1 SMC-83_R1.fastq.gz -2 SMC-83_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-84 -1 SMC-84_R1.fastq.gz -2 SMC-84_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-85 -1 SMC-85_R1.fastq.gz -2 SMC-85_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-86 -1 SMC-86_R1.fastq.gz -2 SMC-86_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-87 -1 SMC-87_R1.fastq.gz -2 SMC-87_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-88 -1 SMC-88_R1.fastq.gz -2 SMC-88_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-89 -1 SMC-89_R1.fastq.gz -2 SMC-89_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-9 -1 SMC-9_R1.fastq.gz -2 SMC-9_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-90 -1 SMC-90_R1.fastq.gz -2 SMC-90_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-91 -1 SMC-91_R1.fastq.gz -2 SMC-91_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-92 -1 SMC-92_R1.fastq.gz -2 SMC-92_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-93 -1 SMC-93_R1.fastq.gz -2 SMC-93_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-94 -1 SMC-94_R1.fastq.gz -2 SMC-94_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-95 -1 SMC-95_R1.fastq.gz -2 SMC-95_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-177 -1 SMC-177_R1.fastq.gz -2 SMC-177_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-178 -1 SMC-178_R1.fastq.gz -2 SMC-178_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-179 -1 SMC-179_R1.fastq.gz -2 SMC-179_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-180 -1 SMC-180_R1.fastq.gz -2 SMC-180_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-181 -1 SMC-181_R1.fastq.gz -2 SMC-181_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-182 -1 SMC-182_R1.fastq.gz -2 SMC-182_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-183 -1 SMC-183_R1.fastq.gz -2 SMC-183_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-184 -1 SMC-184_R1.fastq.gz -2 SMC-184_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-185 -1 SMC-185_R1.fastq.gz -2 SMC-185_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-186 -1 SMC-186_R1.fastq.gz -2 SMC-186_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-187 -1 SMC-187_R1.fastq.gz -2 SMC-187_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-188 -1 SMC-188_R1.fastq.gz -2 SMC-188_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-189 -1 SMC-189_R1.fastq.gz -2 SMC-189_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-19 -1 SMC-19_R1.fastq.gz -2 SMC-19_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-190 -1 SMC-190_R1.fastq.gz -2 SMC-190_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-191 -1 SMC-191_R1.fastq.gz -2 SMC-191_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-20 -1 SMC-20_R1.fastq.gz -2 SMC-20_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-21 -1 SMC-21_R1.fastq.gz -2 SMC-21_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-22 -1 SMC-22_R1.fastq.gz -2 SMC-22_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-23 -1 SMC-23_R1.fastq.gz -2 SMC-23_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-24 -1 SMC-24_R1.fastq.gz -2 SMC-24_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-25 -1 SMC-25_R1.fastq.gz -2 SMC-25_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-26 -1 SMC-26_R1.fastq.gz -2 SMC-26_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-27 -1 SMC-27_R1.fastq.gz -2 SMC-27_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-28 -1 SMC-28_R1.fastq.gz -2 SMC-28_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-29 -1 SMC-29_R1.fastq.gz -2 SMC-29_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-3 -1 SMC-3_R1.fastq.gz -2 SMC-3_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-30 -1 SMC-30_R1.fastq.gz -2 SMC-30_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-31 -1 SMC-31_R1.fastq.gz -2 SMC-31_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-32 -1 SMC-32_R1.fastq.gz -2 SMC-32_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-33 -1 SMC-33_R1.fastq.gz -2 SMC-33_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-34 -1 SMC-34_R1.fastq.gz -2 SMC-34_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-35 -1 SMC-35_R1.fastq.gz -2 SMC-35_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-36 -1 SMC-36_R1.fastq.gz -2 SMC-36_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-37 -1 SMC-37_R1.fastq.gz -2 SMC-37_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-38 -1 SMC-38_R1.fastq.gz -2 SMC-38_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-39 -1 SMC-39_R1.fastq.gz -2 SMC-39_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-4 -1 SMC-4_R1.fastq.gz -2 SMC-4_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-40 -1 SMC-40_R1.fastq.gz -2 SMC-40_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-41 -1 SMC-41_R1.fastq.gz -2 SMC-41_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-42 -1 SMC-42_R1.fastq.gz -2 SMC-42_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-43 -1 SMC-43_R1.fastq.gz -2 SMC-43_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-44 -1 SMC-44_R1.fastq.gz -2 SMC-44_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-45 -1 SMC-45_R1.fastq.gz -2 SMC-45_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-46 -1 SMC-46_R1.fastq.gz -2 SMC-46_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-47 -1 SMC-47_R1.fastq.gz -2 SMC-47_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-48 -1 SMC-48_R1.fastq.gz -2 SMC-48_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-49 -1 SMC-49_R1.fastq.gz -2 SMC-49_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-5 -1 SMC-5_R1.fastq.gz -2 SMC-5_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-50 -1 SMC-50_R1.fastq.gz -2 SMC-50_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-51 -1 SMC-51_R1.fastq.gz -2 SMC-51_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-52 -1 SMC-52_R1.fastq.gz -2 SMC-52_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-53 -1 SMC-53_R1.fastq.gz -2 SMC-53_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-54 -1 SMC-54_R1.fastq.gz -2 SMC-54_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-55 -1 SMC-55_R1.fastq.gz -2 SMC-55_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-56 -1 SMC-56_R1.fastq.gz -2 SMC-56_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-57 -1 SMC-57_R1.fastq.gz -2 SMC-57_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-58 -1 SMC-58_R1.fastq.gz -2 SMC-58_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-59 -1 SMC-59_R1.fastq.gz -2 SMC-59_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-6 -1 SMC-6_R1.fastq.gz -2 SMC-6_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-1 -1 SMC-1_R1.fastq.gz -2 SMC-1_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-101 -1 SMC-101_R1.fastq.gz -2 SMC-101_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-11 -1 SMC-11_R1.fastq.gz -2 SMC-11_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-161 -1 SMC-161_R1.fastq.gz -2 SMC-161_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-162 -1 SMC-162_R1.fastq.gz -2 SMC-162_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-163 -1 SMC-163_R1.fastq.gz -2 SMC-163_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-164 -1 SMC-164_R1.fastq.gz -2 SMC-164_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-165 -1 SMC-165_R1.fastq.gz -2 SMC-165_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-166 -1 SMC-166_R1.fastq.gz -2 SMC-166_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-167 -1 SMC-167_R1.fastq.gz -2 SMC-167_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-168 -1 SMC-168_R1.fastq.gz -2 SMC-168_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-169 -1 SMC-169_R1.fastq.gz -2 SMC-169_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-17 -1 SMC-17_R1.fastq.gz -2 SMC-17_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-170 -1 SMC-170_R1.fastq.gz -2 SMC-170_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-171 -1 SMC-171_R1.fastq.gz -2 SMC-171_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-172 -1 SMC-172_R1.fastq.gz -2 SMC-172_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-173 -1 SMC-173_R1.fastq.gz -2 SMC-173_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-174 -1 SMC-174_R1.fastq.gz -2 SMC-174_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-175 -1 SMC-175_R1.fastq.gz -2 SMC-175_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-176 -1 SMC-176_R1.fastq.gz -2 SMC-176_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-18 -1 SMC-18_R1.fastq.gz -2 SMC-18_R2.fastq.gz
salmon quant -i mm_gencode_36 -p 12 -l A --validateMappings --gcBias -o SMC-2 -1 SMC-2_R1.fastq.gz -2 SMC-2_R2.fastq.gz

Conclusion

Salmon version 1.10.0 was used for quantification. The output for each sample, including the crucial quant.sf, which are the input for the next R-based processing step to generate a gene-level count matrix for downstream analysis.

Data Processing: Download, Indexing, and Quantification

Qingzhou Zhang, PhD

2025-04-10