I used prefetch to get the Pacbio reads of chicken from the SRA database. I want to align these reads against a reference genome, but not all the reads. I am only interested in a particular region on Chromosome Z. Is there a way that I can subset the downloaded SRA file?
I am trying to use blast, but don't know where to start. How should I prepare the SRA file from prefetch for the blast? I have currently started fasterq-dump for the downloaded SRA file.
Or should I subset after aligning the entire SRA reads data with the reference genome, and in that case what tools do I use?