[maker-devel] est_forward and conflicting names

[Shaun Jackman]

Hi, Carson. Could you give an example of how to add gene_id= to the header
of the FASTA file? I’m not clear on what you mean by this. In the FASTA
header, what portion is the transcript name, and what portion is the gene
name?

Cheers,
Shaun

*http://sjackman.ca <http://sjackman.ca>*


On 2 May 2014 11:55, Carson Holt <carsonhh at gmail.com> wrote:

> 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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