Downloading single cell RNASeq data using SRA
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Entering edit mode
13 months ago
Apoorva ▴ 310

Hi,

I'm trying to download a single cell RNASeq dataset from GEO to run my analysis on them. I need the 3 fastq files to begin with (R1, R2 and I1).

prefetch SRR9313701

I used sra toolkit and got the .sra file using the prefetch command and then I ran fastq-dump to split them.

fastq-dump --split-files SRR9313701.sra

I got 3 files - SRR9313701_1.fastq, SRR9313701_2.fastq and SRR9313701_3.fastq. Now should i assume SRR9313701_1.fastq is R1, SRR9313701_2.fastq is R2 and SRR9313701_3.fastq is I1 ? If not, how do I get them in the original format with the original names ?

Is there a better way to get raw fastq files of single cell data from GEO ?

Thanks, Apoorva

single cell RNASeq sra toolkit • 1.2k views
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Entering edit mode
13 months ago
ATpoint 54k

Yes, that sounds about right, see https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR9313701

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