Download public single-cell RNA-seq fastq from GEO

Question

[dahun73]

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!

Answer 1

[GenoMax]

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.