Can cell ranger count take a folder of only .fastq.gz as input?
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16 months ago
jrleary ▴ 170

I'm attempting to run cellranger count on some fastq files provided to me by a colleague from a different lab. Every other time I've processed single cell data I've done every step myself, from sequencing -> downstream analysis. Typically when running cellranger count I specify the subdirectory the fastq are located in, within a larger directory that contains logs and other information concerning the sequencing run. Would it be possible to run cellranger count on a directory that contains just fastq files without any of the supplementary files? I'd test on a single file but I need to transfer the fastq to a cluster first and that's going to take a while, so I'd prefer to know beforehand if it's going to work or not, and also if I need to request for my colleague to provide all the other relevant files.

cellranger scRNAseq • 793 views
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Entering edit mode
16 months ago
swbarnes2 9.7k

Cellranger doesn't need those logs. Just the fastqs.

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