Dear all,
I have a gff annotation file with coordinates for an overlapping genomic feature, e.g.
chr1 1-100
chr1 100-250
chr1 250-300
chr1 300-500
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,
chr1 50-70
chr1 90-110
chr1 150-170
chr1 245-255
Only extract
chr1 90-110
chr1 245-255
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.
Thanks
Search this site/the web for bedtools intersect
Thanks for the idea, Istvan Albert. That actually makes a lot of sense. I can do that.
Thanks again