Question: Not able to read 10x data
gravatar for sidrah.maryam
14 days ago by
sidrah.maryam20 wrote:

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 • 90 views
ADD COMMENTlink written 14 days ago by sidrah.maryam20

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

ADD REPLYlink written 14 days ago by e.rempel980

Thanks for your response.

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

ADD REPLYlink written 14 days ago by sidrah.maryam20
gravatar for e.rempel
14 days ago by
Germany, Heidelberg
e.rempel980 wrote:

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.

ADD COMMENTlink written 14 days ago by e.rempel980

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.

ADD REPLYlink written 14 days ago by sidrah.maryam20
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