[maker-devel] [CAUTION: Suspicious Link] map_forward=1 not mapping reference ID's to output correctly

[Poelchau, Monica]

Hi Kapeel,

If you just want your community annotations to replace models in an existing gene set, we have a tool for this:

https://github.com/NAL-i5K/GFF3toolkit

You’d need to run gff3_QC on your annotation files first to make sure your annotations are okay, then use gff3_merge to merge your community annotations with your existing gene set (in gff3 format). If you end up trying this out - we’re actively developing the GFF3toolkit, so feel free to post an issue if you notice any problems.

Hth,

Monica

From: maker-devel <maker-devel-bounces at yandell-lab.org> on behalf of Kapeel Chougule <kapeelc at gmail.com>
Date: Friday, June 22, 2018 at 13:53
To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject: [CAUTION: Suspicious Link][maker-devel] map_forward=1 not mapping reference ID's to output correctly


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Hi,

I am trying to update community annotation<https://de.cyverse.org/dl/d/39D60E88-078D-4CF5-9F3A-D712B714CDD8/community.annotation.gff3> in the light of new evidence data but my MAKER runs are not keeping all the genes from the community annotation.


Community annotation feature count: 2 1 bicolor 239969 CDS 266301 exon 51066 five_prime_UTR 34129 gene 47121 mRNA 53708 three_prime_UTR
MAKER gene count->
awk '$3=="gene"{print}' maker_output.all.gff | grep "Sobic*" | wc -l 21105

In the maker_opts.ctl file attached, I did make keep_preds=1 and map_forward=1 which keep all the community gene models even if they dont have evidence support. This was explained here:
http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data
. So not sure why we dont have the all the community gene models mapped in the MAKER output

Thanks

Kapeel
--

Kapeel Chougule
Computational Scientist Developer II
One Bungtown Road Cold Spring Harbor, NY 11724
http://www.warelab.org/




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