I am trying to use Faster Download and Extract Reads in FASTQ to download single-cell RNA-seq raw reads. The specific SRR accession is SRR11821880, and the SRA run browser tells me that there are three reads per spot. The first two are technical reads (adapter: 8 bp, barcode+UMI: 28 bp), and the last one is a biological read (150 bp).
My settings for the tool are:
- Select input type: SRR accession
- Advanced options>Select how to split the spots: --split-files
- Advanced options>Dump only biological reads: No
Currently, I am only getting the fastqs with the adapter sequences and the biological reads, but not the barcode+UMI. I’m unsure of why this is happening, since I am able to browse and view all of the reads in the run browser. Is this tool restricted to getting only two files maximum, or am I overlooking a setting?