[maker-devel] AED scores and thresholds: Not filtering?

[Carson Holt]

No.  It should use whichever is lower the AED or eAED score.  The only
exception is model_gff results.  Those are always kept.  Also note that the
filter is for the entire gene, not just individual splice forms if you have
alternate splicing.

If you want I can take a look if there is anything non-obvious.  You would
have to send me the final GFF3 and the maker_opts.ctl file.

--Carson


From:  Jan Philip Øyen <janphilipoyen at gmail.com>
Date:  Tuesday, June 3, 2014 at 9:07 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] AED scores and thresholds: Not filtering?

Hello,
We are currently working on annotating arthropod genomes with the maker
pipeline. We have tried to filter out genes with low support using the AED
thresholds using AED_threshold=0.5. However, we still find genes without
scores and most importantly genes with scores above the set threshold (even
AED=1). Is there a known issue which could cause this?

We can supply the control files as well as gffs, but would not like to make
them public at this stage.

Best Regards,
Jan Philip Oeyen
ZFMK / ZMB / University of Bonn
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