single-end read for scRNA-seq data

Question

[dahun73]

Hello :)

I tried to download and analyze scRNA-seq data in GEO. However, some files are single-end data. I think these are already demultiplexed. Normally, there are 3 files, R1, R2, and I1(optional). Is it possible scRNA-seq data have only one fastq file? If it can, how should I process these fastq files?

The data that I mentioned in here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE124952

Thanks

Answer 1

[ATpoint]

The 10x bam file is available per sample, see https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR8433705&display=data-access at the bottom

You can get that via prefetch (or direct doenload) and convert back to fastq to get both R1 and R2, see https://bioinformatics.stackexchange.com/a/15523