How to find/filter intron-retained reads from BAM files? Which flag in BAM file describes information about retained intron.
I know there are some tools to find retained intron, but i want to understand how they are represented in BAM files.
When there is an intron retention, portion of reads map to exon and remaining to intron. Is this correct?
Which flag in BAM file describes information about retained intron.
The SAM/BAM file format has no standard fields for retained intron reads. Any such fields will be custom fields for the aligner or detection tool used.
but i want to understand how they are represented in BAM files.
SAM/BAM files contain the read sequence, base qualities, alignment location, any optional standard or custom SAM tags. The SAM/BAM format itself does not include any reference genome annotation information (such as genes, exons, introns, repeats, and so on). You need to get this information from other annotation files.
