Introns from Exons of GTF File
1
0
Entering edit mode
6.4 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 • 7.8k views
ADD COMMENT
0
Entering edit mode
ADD REPLY
0
Entering edit mode

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.

ADD REPLY
2
Entering edit mode
6.4 years ago
ATpoint 86k

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

chr1 start end

chr2 start end

(...)

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

I keep it in mind, thanks!

ADD REPLY

Login before adding your answer.

Traffic: 2549 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6