I'm deeply sorry if my question was obscure: what I want to do is to get, from an alignment, reads without nucleic bases before position 30 of the reference sequence. Is it possible to crop a bam file?
would it be possible to resolve this problem using an awk script?
I was thinking of an alignment, conversion to fasta (with gap or x for non-aligned bases) and then trimming using awk or fastx_trimmer? Maybe there is something easier? how do I get gap or 'x' for non-aligned bases before and after each reads?