I'm looking for an alignment containing reads started or clipped at the first position and ended or clipped at the last position of my alignment. I don't want to have reads ended in the middle of the sequence.
For that I've done an alignment from fastq input with bwa on my entire gene, then selected a region between 2 positions (samtools view -b trialsorted.bam AA_AD:30-230 > trialsorted30-230.bam) and then realign these sequences with a reference containing only the first bases of my start position and the same for the last bases of my end position in order to keep only reads of interest. However I didn't get a selection of sequences starting from a position and ending to another position.
Does anyone have any idea how to solve my problem?