SRAtoolkit --split-files output

Question

[tony_88888]

Hi,

I've been using sratoolkit for a while now but still get confused by the output at times. For example, I am trying to download the accession SRR12386358. This is paired end data and looking at the 'data access' tab it looks like they have deposited the data correctly with fastqs for read 1 and 2

link to accession https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&page_size=10&acc=SRR12386358&display=data-access

When I use fastq-dump --split-files --readids I get 3 files output. Please see headers in the picture attached. Could someone please explain to me which each one of these files is? Is there a way to get these files in a format that I can use for cellranger? I have tried --split-3 but the output is a single file and similar output using fasterq-dump.

Answer 1

[GenoMax]

_1 file is the Illumina barcode for the sample, which is not used by cellranger.
_2 file is the Cellbarcode + UMI
_3 is the RNA read

If you had used -F with normal fastq-dump you would have removed @SRR part and ended up with normal Illumina fastq headers.

Answer 2

[tony_88888]

Thank you very much for the response.

Do you have any idea why I got that output and not the expected read 1 and read 2? Can these files still be used as they are in cellranger or do I need to try and download them again with sratoolkit?