I have a gff annotation file with coordinates for an overlapping genomic feature, e.g.
and an alignment file (bam/bed) with reads mapping to that chromosome. I need to extract reads that are specifically overlapping the junctions of that genomic feature. So, in a bed file like this,
Any existing tools that can help me do that. I know bedtools intersect will give me all the common overlap but I am only looking for reads mapping the junctions of concurrent genomic features. I am not well versed in bioinformatics so I can't write my own scripts but am able to run existing tools.
Any ideas would be appreciated.