Cellranger count command for single end fastq
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3.4 years 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 • 3.4k 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 ?

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Just my two cents here. In my case cellranger count was failing because R1 was in the wrong format. I also had single-end reads, where R1 was supposed to be the cell barcode and UMI, and R2 should be the single-end reads. In my case I had to rerun cellranger mkfastq from the raw BCLs. Note that the I1 file mentioned is optional for cellranger count so don't worry if you don't have it.

In my experience the --split-files option for fastq-dump is only relevant if you're downloading data from SRA, not if you have your raw data in-house.

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In my experience the --split-files option for fastq-dump is only relevant if you're downloading data from SRA, not if you have your raw data in-house.

Please read the question - OP has SRR identifiers, hence their data is from SRA. That is why GenoMax mentioned the --split-files.

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