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access original uploaded bam files from SRA?

Open whtns opened this issue 9 months ago • 0 comments

Hi, thanks for this great tool. Is it possible to access the original uploaded files for an accession in SRA? I am trying to recover raw fastqs from 10x samples uploaded as bams to SRA. I am told by SRA that "The SRA does not properly preserve all 10X bam flags when archiving aligned 10X data. The SRA is therefore not able to correctly serve 10X data that is submitted in an aligned format via the SRA Toolkit. Because of this, the SRA makes the originally submitted files available for download directly from the SRA Run pages. For example:https://www.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&acc=SRR11546787&display=data-access

Is it possible to recover these original bams with ffq? Are you aware of another tool to achieve this?

Thanks for any help!

whtns avatar May 07 '24 00:05 whtns