[maker-devel] est_forward and conflicting names

[Carson Holt]

Whichever has the best AED score I believe, but you can add gene_id= to the
header of each fasta file to ensure MAKER doesn't try and cluster unrelated
transcripts into a single gene.  Then the transcript name and gene name will
be guaranteed to match up.

--Carson


From:  Shaun Jackman <sjackman at gmail.com>
Date:  Wednesday, April 30, 2014 at 5:25 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] est_forward and conflicting names

Hi, Carson.

I’ve downloaded a number genes from GenBank using Entrez Direct, which I’m
using with est and protein to annotate a plant mitochondrion. Most of these
reference sequences have sensible and consistent gene names, and so I’m
using est_forward to retain the gene names. This workflow is working well
for me. Some of the genes pulled in from GenBank have less useful names like
orf1234 or other numeric IDs. When multiple evidence sequences map to the
same location, how does est_forward choose which name to use? If it’s chosen
arbitrarily, could it be possible to choose the most common name instead?

Thanks,
Shaun



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