I would like to run bwa in my reads (12 pair end reads = 24 samples) and create a .sam file as an out put.
I want to use the command:
bwa sampe ref.fa aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln-pe.sam
My question is if I can use an unique command for all my 12 pair reads or I have to run 12 different commands (one per pair end read).
Any help is more than welcome :)