How to rename fastqs for cell ranger ?

Question

[Meghamsh]

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 ?

Answer 1

[GenoMax]

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.

[Meghamsh]

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.

[Mauricio]

If you go to https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRRXXXXXXXX you should be able to the metadata page for the run. There you will see how the reads are divided and hopefully lane and run information explicitly as in the highlighted spots. It still seems like a bit of a hassle to rename manually, if anyone knows how it would be appreciated.