Cellranger count command for single end fastq
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4 months ago

Hello everyone, I have single end sequence fastq files that were processed using cellranger. Now I need to align them using cellranger count function. But being single end, the naming convention followed could not be standard. Is there a way to do so? I tried using SRR9320581_S1_L001_R1_001.fastq.gz file convention, but it gave pipestance failed error.

Any help is highly appreciated. Thank you

RNA-Seq sequencing • 324 views
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cellranger count needs files in a special format. There are three separate files (if you have > 1 sample). R1 file contains the cell barcodes and UMI, I1 file contains Illumina index for the sample, R2 file contains actual reads. It appears that these investigators may have submitted these fastq files in a concatenated format. Try to see if you can separate the reads using --split-files option for fastq-dump.

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okay. I will try that. Thanks a lot.

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I have the same issue, did the split-files solved your problem ?