This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Download public single-cell RNA-seq fastq from GEO

Hello everyone!

I have a question about downloading scRNA-seq from GEO. Actually, I used 'fastq-dump' command. But there are two fastq files for sample, R1 and R2.

I used this command. $ fastq-dump --gzip --split-files SRR5945694

Did I use wrong command?

Thank you in advance!

rna-seq single-cell

1 answer

That looks correct. If you check the SRA record it shows that there are two reads. R1 = 35 bp and R2= 51 bp. inDrops protocol is described in this paper.

Log in to answer this question.