[maker-devel] Maker output

[Panos Ioannidis]

Hello Maker community,

I have, at last, finished annotating my genome with Maker (!) and have a
few questions on the final output.

1. I used gff3_merge and fasta_merge in order to merge all the gffs and all
the different fasta files that were produced during the runs (I split my
assembly to smaller chunks that ran in parallel). Are these two scripts the
only ones I have to run after Maker has finished? Am I leaving anything
important behind?

2. I noticed that all my transcripts (both in the fasta files as well as in
the gff) have the name "XXX-mRNA-1". The fact that I can't find any of them
containing "mRNA-2" means that there are no splice variants from the same
gene?

3. In my *maker.proteins.fasta file I see that some proteins have a name
like

snap_masked-XXX

whereas others (apparently, also predicted by SNAP) have a name, like

maker-XXX-snap-gene-XXX

What is the difference between these two genes that are both predicted by
SNAP? By reading other posts in this list, I was left with the impression
that all genes predicted by SNAP/Augustus that lie in a masked region (as
the first name implies), are put to another fasta file, named
*maker.snap_masked.proteins.fasta.

4. By looking at a few genes in the *maker.transcripts.fasta file I came to
the conclusion that only complete genes (i.e. with a start and a stop
codon) are reported in this file. Am I right?

Thanks in advance,
Panos
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