[maker-devel] antisense RNA in training set?

[Steven Sullivan]

My organism's genome is predicted to have extremely few introns.  Does that
mean I should change the default alignment behavior for single exons?

On Tue, Sep 6, 2016 at 4:09 PM, Carson Holt <carsonhh at gmail.com> wrote:

> MAKER does not require input evidence to be on the correct strand because
> it performs splice aware alignments via Exonerate against both strands
> (reverse transcription for the second alignment happens internally).
> Exonerate should always map spliced alignments to the right strand because
> it is not be possible to get correct splicing on the opposite strand
> (splice sites are a stranded feature). The only alignments that are
> ambiguous are single exon alignments. They are ignored by default, but when
> not ignored they are stranded to the sequence with the longest canonical
> ORF.
>
> —Carson
>
>
>
> > On Sep 6, 2016, at 1:37 PM, Steven Sullivan <sullis02 at nyu.edu> wrote:
> >
> > I have a set of assembled transcripts from a stranded RNA seq run that I
> want to use for gene finder training in a MAKER run on 'new' organism.
> >
> > I've noticed though that some of my assembled transcripts actually
> appear to be antisense RNAs.
> >
> > Should I include these in the training set?
> >
> >
> >
> >
> > _______________________________________________
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>
>


-- 
Dr. Steven Sullivan
Center for Genomics & Systems Biology
New York University
12 Waverly Place
New York, NY 10003
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