[maker-devel] default gene model by quality_filter.pl is the same with those by setting keep_preds=0?

[Quanwei Zhang]

Hello:

I am following the Maker protocol (2014) to rescue rejected gene models. I
set keep_preds=1 when I ran Maker, and then used "quality_filter.pl -d" to
get the "default" Maker report. According to the annotation it will "Prints
transcripts with an AED <1".

But in a previous post (the link below), it was said "there are models with
AED less than 1 that get rejected for other reasons. ... For example if the
only evidence is a protein alignment that has deep overlapping HSPs
(extremely low complexity alignment) it will be filtered out even though
AED is not technically equal to 1. Also if the overlapping protein evidence
is in a different reading frame than the model it is supposed to support
then the AED will be less than 1 but eAED will be 1 (extended AED), and the
model will be rejected."

*So I wonder, whether the "default" result obtained by "quality_filter.pl
<http://quality_filter.pl>" are really the same as those achieved by
setting  keep_preds=0? Will the script also consider other reasons besides
"*
*AED <1"?*

https://groups.google.com/forum/#!searchin/maker-devel/The$20reason$20there$20are$20differences$20between$20the$20runs$20is$20that$20there$20are$20models$20with$20AED$20less$20%7Csort:relevance/maker-devel/97aNJkT3bgk/W0MEyqEZAAAJ

Thanks

Best
Quanwei
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