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

[Kapeel Chougule]

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 ChouguleComputational Scientist Developer II*


*One Bungtown Road Cold Spring Harbor, NY 11724http://www.warelab.org/
<http://www.warelab.org/>*
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