Intron size from gtf/gff file ?

Question

[Picasa]

Hello,

I have an annotation file produced by maker (gff).

I am looking for a script that either extract the intron sequence (all combined) per gene or the intron total size per gene.

I am kind of stuck with this, so I would be grateful with any help.

Thanks

[GenoMax]

How to find intron co-ordinates from the gff file?

[Malcolm.Cook]

Do you possibly mean per transcript?

When a "gene" has multiple isoforms/transcripts, it is not clear what is meant by the intron sequence of the gene, since the same underlying sequence can be intronic in one transcript and coding or in another.

Some people intend to mean sequence which is intronic in every isoform. Some, in any isoform. Some really want to tabulate by transcript. Which is your case?

You might find an answer to your question in my answer to this similar question: how to get intronic and intergenic sequences based on gff file?

Answer 1

[Hussain Ather]

This should do the trick https://github.com/irusri/Extract-intron-from-gff3