Get introns in bam format from alignment reads result

Question

[xd_d]

Hey all,

I have alignt rna-seq data with Star against the reference genome hg38. Now I have the results in bam format.

Does anyone know if there is a program that can that detect the introns from the alignment result. Finally I want the only introns in a bed file that are mapped against the reference genome. Before I start programing I want ask if somebody know about nice tools ?

[Devon Ryan]

What is your actual end goal?

[Benn]

I usually extract reads mapped to exons from BAM files with featureCounts using a gtf file from ENSEMBL. So my guess is that you can also extract the reads that map to the introns only with featureCounts.

[GenoMax]

This question is not entirely clear if you are just looking get known exons as a BED file or are looking to find new exons that may be represented in your file file. If it is the former then these directions are still valid. Otherwise you are going to need to look for split-read mappings in your file.