Hi everyone, here's my question:
I have some BAM files resulting from mapping RNA-seq reads. I would like to know whether there is a way to extract the reads mapping within defined intronic regions.
When simply doing "samtools view file.bam chr1:Start-End > result.bam", I get reads in the output file even if there are no actual reads mapped within the intronic region of interest, this is a result of the fact that samtools outputs also read fragments spanning from one exon to another, and not mapping inside the intron; while I would like to know which reads map within a given intronic region.
Does anyone know how I may do this?
Thank you in advance.