Get Introns from a gft annotation file

Question

[xd_d]

Hey all,

i have a question how i get the intron coordinates from Hg38 in bed file or bam . Have anybody a Workflow ?

thanks all :)

[WouterDeCoster]

Hi xd_d,

It's always best to show what you tried to solve your issue, people will be more eager to solve your bugs and help you if you show some effort from your side.

Cheers,
Wouter

Answer 1

[Saber HQ]

If you have the gff3 file, you may use the GenomeTools with the following command to include intron coordinates in the gff3 file format. Later you may also convert it to gtf if you want.

gt -gff3 -retainids -addintrons input_gff3 > output_gff3

[michael.j.apostolides]

Seems the command has changed slightly. It now is as follows (the "-gff3" flag is now its own tool "gff3":

gt gff3 -retainids -addintrons input_gff3 > output_gff3

[mathieuq]

This works really well - exactly what I was looking for!

Answer 2

[xd_d]

I found this script on https://github.com/riverlee/IntronGTF and used that to get the introns.

thanks all