How to rename fastqs for cell ranger ?
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7 weeks ago
Meghamsh • 0

I'm bit new to cell ranger. I have tried using public datasets and download raw fastq files in SRA run selector ( by copy-pasting experiment number in European nucleotide archive). They have names like SRRXXXXXXX.fastq.gz. I tried to follow the cell ranger naming format for the same but am struck at the part on how to name the sample, lane name and the read type. Where can i find information for these ?

cell genomics count ranger fastq 10x • 223 views
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7 weeks ago
GenoMax 107k

You will have three or four files per sample depending on the type of 10x data you are dealing with. There can be lane specific files, if a sample ran on multiple lanes. You can find examples of how the files should be named at this link.

Basic format needs to be:
Files from lane 1 - sampleID_S<number>_L001_<R1/R2/I1>_001.fastq.gz.
Files from lane 2 - sampleID_S<number>_L002_<R1/R2/I1>_001.fastq.gz.

you get the idea.

< > in name above indicates that each file name will have one value.

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Thanks for the response. For example, I want to run this data. Where can I get details for which lane it belonged to and the read type.

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