Introns from Exons of GTF File

Question

[gtasource]

I have a GTF file where I have filtered everything besides the exon coordinates. I know want to get the intronic regions in between all of those exons. What would be the easiest way of achieving this?

Thanks!

[GenoMax]

See if this helps: Get Introns from a gft annotation file

[gtasource]

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.

Answer 1

[ATpoint]

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.

[gtasource]

Thank you ATpoint. I must have missed your post when I did my original search. Cheers!

[gtasource]

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.

[ATpoint]

Yes, just that the entries itself are separated by "\n", so each chromosomes gets a new line:

chr1 start end

chr2 start end

(...)

[gtasource]

Thanks! Im still getting the "exceeds the length of chromosome." Do you think I should change it from 0 to 39238 to 1 to 39238. Or even subtract one from the sizes? Kind of confused as to why it's saying it's exceeding the length.

[ATpoint]

Are you sure that your GTF file and the chromosome borders you use are from the same genome version? What organism is this?

[GenoMax]

@ATpoint: You can deep link a particular post/comment. I changed your link to directly point to your answer in the other thread.

[ATpoint]

I keep it in mind, thanks!