exon cordinates

[cmccabe]

Is there a perl script to find the exon coordinates of a bed file?

So, can a bed file of 4503 genes be used as an input an the output is the exon locations of those genes? Thanks.

[dpryan]

bedtools intersect could do that and you wouldn't even need to muck with perl. This is also easy in R (using rtracklayer to import both files as GRanges objects and then just using findOverlaps()).

[cmccabe]

I am familiar with that command and will read up on it more. I have only used it to merge and intersect two bed files so far. Thanks.