Multiple paired-end files as input

[zji90]

Hi, The example 'Files_to_process.txt' only includes one file: /home/pbost/Desktop/Viral_Track/Data_COVID/C147_S1_L001_R2_001.fastq.gz If I have multiple paired-end reads from multiple lanes (which is typical for 10x experiments), such as: sample_S1_L001_R1_001.fastq.gz sample_S1_L001_R2_001.fastq.gz sample_S2_L001_R1_001.fastq.gz sample_S2_L001_R2_001.fastq.gz

How should I specify Files_to_process.txt? Thank you!

[PierreBSC]

Hi Zhicheng,

To process 10X data you only have to put the R2 files as the R1 file only contains the barcode. However if you wish to perform single-cell demultiplexing you have to label the reads using umi_tools whitelist and extract commands. This is described extensively on this webpage : https://github.com/CGATOxford/UMI-tools/blob/master/doc/Single_cell_tutorial.md

So here for the Files_to_process.txt should look like : sample_S1_L001_R2_001.fastq.gz sample_S2_L001_R2_001.fastq.gz Hope this will help you !

Best

Pierre

[zji90]

Thank you!