I was trying to get started with scRNA seq analysis. I downloaded a test dataset from bioproject (NCBI). However, each sample is in three fastq files (e.g. SRR123_1.fastq.gz, SRR123_2.fastq.gz, SRR123_3.fastq.gz).
How do I process these in Kallisto? Do I need to combine all of these files (how?), or split each file into forward and reverse reads before combining?
Else, what fastq-dump command do I need to issue to download the forward and reverse reads as separate files? My current command is:
fastq-dump -I --split-files SRR123