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Make bed files for different functional group given GFF3 file

Hi!

I am trying out something new and am already a little stuck. Any assistance would be really appreciated.

I have whole genome sequencing data for a number of samples, which I have already mapped to the reference assembly for my study species. These are currently in sorted bam files. I would now like to compare sequencing read depth across three 'functional groups'; exons, introns and intergenic regions. My annotations are in a GFF3 file. From reading around I have gathered that I should make three bed files, one pertaining to each functional group.

What I would like to know is how to prepare these bed files using the GFF3 file. Could anyone point me in the right direction?

Many thanks!

alignment annotations functional groups exon gff
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written by rc16955 rc16955

Hello rc16955!

We believe that this post does not fit the main topic of this site.

This question has been asked multiple times before, see e.g.:

Get intronic and intergenic sequences based on GFF file

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by ATpoint ATpoint

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