Question

sc-RNA seq DATA

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12 months ago

Researcher ▴ 30

Hello,

I am trying to download single cell RNA seq data from NCBI-SRA. The meta data says its paired end data, but when I download using fastq-dump --split-files command, only one file is getting generated. and in addition meta data specifies it has one read per spot. when I tried running this one fastq file in cell ranger tool, it showed error- asking for paired end file. What to do ? How to work with sc-RNA seq data?

scRNA-seq NGS RNA-Seq • 1.1k views

ADD COMMENT • link 12 months ago by Researcher ▴ 30

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Which accession?

ADD REPLY • link 12 months ago by ATpoint 86k

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SRR10852476-SRA accession ID

ADD REPLY • link 12 months ago by Researcher ▴ 30

score 3 · Accepted Answer · 2023-12-27

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12 months ago

ATpoint 86k

Single-cell data upload to NCBI is always pretty violent. Often one read is missing.

Easiest is to download the 10x BAM file that is included in the submission: https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR10852476&display=data-access

It's under "Original format" at the link. Then use https://www.10xgenomics.com/support/software/cell-ranger/miscellaneous/cr-bamtofastq to get original fastq files from that.