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Not able to read 10x data

Hello everyone, I have a few samples of 10x data which I am running using cellranger pipeline. All the samples got converted easily, however, one of the samples is not being read. I have checked its path, it is all correct, also I converted the file from the SRA toolkit in order to avoid any corruption.

I used the command line:

cellranger count --id=SRR11194349 --transcriptome=/home/sid

rah19220/princy/crispr/reference_hg19/hg19 --fastqs=/home/sidrah19220/mouse_a/sraa/sra --sample=SRR11194349 --expect- cells=8000 --localcores=12

And the error I got is:

error: No input FASTQs were found for the requested parameters.

If your files came from bcl2fastq or mkfastq: - Make sure you are specifying the correct --sample(s), i.e. matching the sample sheet - Make sure your files follow the correct naming convention, e.g. SampleName_S1_L001_R1_001.fastq.gz (and the R2 version) - Make sure your --fastqs points to the correct location.

Despite the sample name is correct, path also, and also other samples worked so it is not also the data problem. What could possibly be the reason or suggestion that I should follow. I will be highly thankful to you all.. :) Thanks in advance.

rna-seq
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written by sidrah.maryam • sidrah.maryam

Difficult to tell. Could you show the content of /home/sidrah19220/mouse_a/sraa/sra?

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written by e.rempel e.rempel

Thanks for your response.

That folder just has two files: SRR11194349_S_L001_R1_001.fastq.gz SRR11194349_S_L001_R2_001.fastq.gz

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written by sidrah.maryam • sidrah.maryam

1 answer

One thing I have noticed: the name of the file is SRR11194349_S_L001_R1_001.fastq.gz. I rather expect it to be SRR11194349_S1_L001_R1_001.fastq.gz. Did the other samples also look like this? Maybe you have to manually add the missing 1 in the file's name.

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written by e.rempel e.rempel

Thank you so much. Yes, that was the mistake. I had actually made the script for renaming, and for this sample it got missed. Thanks a lot :) Highly grateful.

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written by sidrah.maryam • sidrah.maryam

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