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Get Introns from a gft annotation file

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 :)

rna-seq intron
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updated by Saber HQ • Saber HQ • written by xd_d xd_d

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

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written by WouterDeCoster WouterDeCoster

2 answers

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

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written by Saber HQ • Saber HQ

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

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written by mathieuq • mathieuq

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

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written by michael.j.apostolides • michael.j.apostolides

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

thanks all

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written by xd_d xd_d

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