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Intron size from gtf/gff file ?

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

intron annotation
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updated by Hussain Ather Hussain Ather • written by Picasa Picasa

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?

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written by Malcolm.Cook Malcolm.Cook

1 answer

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

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written by Hussain Ather Hussain Ather

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