I was trying to experiment a bit with the scrna fastq files from 10x (v3x3). My files are of type:
L001_I1_001.fastq.gz L001_R1_001.fastq.gz L001_R1_001.fastq.gz
Since the full dataset is too large (~ 20,000 cells), is there a way (how) that I can extract fastq data for ~200 cells?
I was thinking of extracting the cell barcodes/whitelist using umi_tools and then just use grep for 200 of the barcodes. This would give me the results for R1, but how will I get the corresponding R2 reads?
Or is there a better way?
thanks for your help