[maker-devel] Running maker with suboptimal evidence

[Martin, John]

Greetings,

     I would like to annotate a worm genome of ~90Mb but the evidence I
have is not all of good quality.  I have 2 high quality protein sets
from previously finished & curated, closely related worms.  I also have
a small amount of RNAseq and some old EST data neither of which give
good coverage of the transcriptome.  And I have a previously run Maker
geneset for this worm that I believe was generated using probably all
nematodes from genbank and that poor set of RNAseq.  I also have a
'fair' set of predictions from running Braker2 using only the high
quality protein data I mentioned.   My opinion that the previous Maker
geneset is of poor quality comes from comparing that geneset to my
recent Braker2 annotations and that RNAseq.

     I would like to try and build an improved annotation for this
assembly but I'm unsure of whether I should use all this evidence, or if
I would be better off not using the low coverage RNAseq, EST data and
previous (questionable looking) Maker geneset.   I'm looking for
opinions on whether I should throw all the evidence I have into Maker or
should I use only evidence that I consider of good quality?


Thanks,

John Martin



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