original single cell data downloaded from GEO yielded only two files with 150bp

Question

[chenglei1865]

Hi,

Recently, I downloaded original single cell data from GEO (SRR13403717), and converted it: fastq-dump --split-files --gzip SRR13403717, two files SRR13403717_1.fastq.gz (40G) and SRR13403717_1.fastq.gz (38G), both files are 150bp, I don't know which one is R1 or R2? additionally, the data size is samller than that showed in the uploaded files.

Could anyone help out? Appreciate!

Answer 1

[PeterWu]

checkout https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&page_size=10&acc=SRR13403717&display=reads

looks first is R1 and second is R2

[ATpoint]

True. You can also "see" that in the data. 10x data have that poly-T stretch in R1 after the CB+UMI sequence (26-28bp depending on chemistry) which is clearly present in the first file of the pair.