[maker-devel] Maker v3.01 change-log + 3'UTR question

[Carson Holt]

2. If I was to improve the annotation of my 3’ UTRs within a certain (non-model species) gff3, is there a particular way or a protocol to follow? I was thinking for example that Lexogen has released their 3’ UTR kit for RNA-seq of the three prime end of transcripts. Would it be possible to feed those reads to maker and somehow suggest that the reads are originating from the three-prime end so that this info is then passed in the gff3 file?


You could pass final models back in as predicted_gff (no UTR on the models), then pass in just the evidence you want as UTR as est_gff (would have to be assembled and not as individual reads). As long as the overlap the pred_gff models, MAKER would try and make UTR out of them. Might be worth an experiment.

—Carson
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