Question: Get Introns from a gft annotation file
0
gravatar for xd_d
3.0 years ago by
xd_d90
xd_d90 wrote:

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 • 2.7k views
ADD COMMENTlink modified 2.2 years ago by Saber HQ20 • written 3.0 years ago by xd_d90
1

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

ADD REPLYlink written 3.0 years ago by WouterDeCoster43k
2
gravatar for Saber HQ
2.2 years ago by
Saber HQ20
Vancouver, Canada
Saber HQ20 wrote:

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

ADD COMMENTlink written 2.2 years ago by Saber HQ20

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

ADD REPLYlink written 13 months ago by mathieuq0
0
gravatar for xd_d
3.0 years ago by
xd_d90
xd_d90 wrote:

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

thanks all

ADD COMMENTlink written 3.0 years ago by xd_d90
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