[maker-devel] Questions about re-annotating

[Michael Campbell]

Hi Malcom,

What you do depends on if you just want to just add three and five prime
UTR to gene models that you are otherwise happy with or if you wan't to use
the RNA-seq data to find new genes and alternatively spliced transcripts.
If you just want to add the UTR you can pass MAKER the current models as
pred_gff= and the RNA-seq data as est_gff=. for this you don't gain much
with repeatmasking.

If on the other hand you want to get more than UTR on current models I
would edit the control file and rerun MAKER in the same directory you ran
before. MAKER will check to see what has already been done and only rerun
what is necessary. For this you do need to repeat mask.

If you want to find alternatively spliced transcripts set alt_splice=1. As
a side note, MAKER is quite conservative in annotating alternatively
spliced transcripts. There must be EST/RNA-seq evidence supporting the
alternative splice to be considered.

Mike

On Tue, Jun 23, 2015 at 12:46 AM, Cook, Malcolm <MEC at stowers.org> wrote:

> Hi,
>
> I am re-running an analysis after having adding
> `est_gff=/path/to/cuffmerge.gff3` and want to ensure the least amount of
> work is re-done.
>
> When I re-run maker, should I provide any additional options.  In
> particular, either "--again" ?
>
> On this subject, I read in
> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Updating_annotations_in_light_of_new_data
>
> "if you are using est_gff= you don't even have to repeat mask."  - does
> this mean I should always run maker with option -RM_off when updating
> annotation?
>
> On a related note, if I have est2genome turned on, what changes to
> configuration should cause exonerate to run?  I'm guessing:
>   adding new est= files
>   turning on alt_splice=1
>
> Thanks!
>
> ~ malcolm_cook at stowers.org
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-- 
Michael Campbell MS, RD.
Doctoral Candidate
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:585-3543
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