Introns from Exons of GTF File
1 answer
You may scroll down a bit on this post, and follow the steps I posted there. In short, intronic regions are the complement of intergenic and exonic regions. Details in the link.
I had one question! For the first part, where you convert the chromosome sizes into a bed file, is it supposed to look something like this:
chromosome1 0 39238 chromosome2 0 42942 chromosome3 0 39239
Reason I ask is when I get to the last step of using bedtools complement, I get a " exceeds the length of chromosome " warning.
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See if this helps: Get Introns from a gft annotation file
I tried using genome tools, but the problem I have with it is will not allow me to use a modified gtf file with only exons. If I go ahead and use the full gtf file, the other issue I run into is overlaps between features. I felt like if there's a way of finding the intron coordinates solely from the exons, it would make things much easier.