[maker-devel] RNAseq - Question for Carson and Jason Staijch

[Jason Stajich]

Hi Jason -

Not sure it makes that much difference if you use MAKER's best scored by
AED as best set of predictions for re-training Augustus or running PASA and
grabbing those with long enough ORFs.  I've never tried head to head to see
how much it matters.

The specifics of running PASA on Maker to improve is basically to avoid
some gene splits and where you like it, add UTRs with a bit more precision.
Both tools have their optimization for finding ORFs within the exon calls
and so it is useful to see how they behave, but the extra effort in setting
up PASA may or may not be worth it.
But in terms of details -- as I recall the main hurdle was getting the
MAKER GFF3 in a format that PASA liked as GFF it imported (you load it as a
previous annotation but basically you want to follow the directions for
"Loading your preexisting protein-coding gene annotations" from
https://pasapipeline.github.io/
I may have had to write a processing script as I can see here - renaming
the UTR features

https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/fixmakergff_for_PASAannot.pl

Then you run the annotation compare part of the PASA pipeline to check and
see how the annotations get updated.

Seems like BRAKER and other strategies may be more informative anyways for
running Augustus. My interpretation of what Carson and MAKER team have
shown that having extra supporting evidence for exoans (protein,
RNAseq/ESTs,conservation) improves and trumps over training the gene
predictors?  I'd love to see hard data on this for a couple of tests in the
future. Maybe we can try it ourselves in the future too.

Jason

On Wed, Apr 22, 2015 at 2:04 PM Jason Gallant <jgallant at msu.edu> wrote:

>  Hi Carson and Jason,
>
> I’ve heard you guys say several times on this list serve that Trinity is
> the preferable option for ESTs (vs. Cufflinks). Does this mean the
> genome-guided or the strict denovo approach?
>
> Second, Jason has mentioned using PASA for generating a “best set of
> annotations” for use in Augustus training.  I have seen his post (and
> repost) of this, however there aren’t many details on how to use PASA to
> accomplish this.  Any chance that you could post a more detailed
> walkthrough on how to approach this?
>
> Best,
> Jason Gallant
>
> —
> Dr. Jason R. Gallant
> Assistant Professor
> Room 38 Natural Sciences
> Department of Zoology
> Michigan State University
> East Lansing, MI 48824
> jgallant at msu.edu
>  office: 517-884-7756
>  _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150427/00aa77a3/attachment-0003.html>