Introns from Exons of GTF File
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5.9 years ago
gtasource ▴ 60

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!

gtf bedtools • 7.2k views
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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.

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5.9 years ago
ATpoint 83k

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.

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

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

chr1 start end

chr2 start end

(...)

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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.

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

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

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I keep it in mind, thanks!

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