merge .fastq.gz files

Hi guys,
it is the first time I have to deal with a paired-end single cell RNA-Seq experiment.
As output of demultiplexing I have (relative to one sample for simplicity) the following files:


My question is: since I have to cat the files may I have to cat the files by lanes (e.g. cat SampleA_L001_R1_001.fastq.gz SampleA_L002_R1_001.fastq.gz > ....) or by R* (e.g. cat SampleA_L001_R1_001.fastq.gz SampleA_L001_R2_001.fastq.gz > ....). I think that is irrelevant. I have to perform --count with Cellranger for 10x v3. I know that there are other tools by in my lab people prefer Cellranger.

Thank you in advance



You should, if you need to for Cellranger, cat them to end up with one file for R1 and one file for R2 and thus do two cat commands, one for each read direction.

R1 is the technical read (barcodes, UMI), and R2 the cDNA, therefore you have to cat the R1s and R2s separately, not like
cat R1 R2 > catted. CellRanger is smart though and can take lane replicates afaik, so you only have to cat if you use software other than CellRanger.

before adding your answer.

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