I am interested in loading the single cell fastq files deposited in
for one sample "young_A_HSPC" there are 4x SRA runs
I downloaded these SRAs with prefetch and then I ran
fastq-dump --outdir fastq --gzip --skip-technical --readids --read-filter pass --dumpbase --split-3 --clip SRA*
I got 4x fastq files with equal size. However, I need the following 4 fastq files to run cellranger
I1: Sample index read (optional) I2: Sample index read (optional) R1: Read 1 R2: Read 2
I do not know what the .fastq files are that I have now. Since they are all 2.2GB I do not think that two of them are the I1 and I2.
How do I proceed?