Re: [Evidencemodeler-users] Add PASA transcript assemblies to EVM

[Brian H. <bh...@br...>]

Hi Tom,

In the latest PASA software, you should have a couple of inputs to leverage.

There's the PASA transcript structures, provided in alignment-gff3 format:

ex.
           mydb_pasa.pasa_assemblies.gff3

which you would include as evidence type 'TRANSCRIPT'

and then you could separately run the process:

Extraction of ORFs from PASA assemblies...
http://pasa.sourceforge.net/#A_train

which should generate a file in protein-coding gene gff3 format:

ex.

   mydb_pasa.assemblies.fasta.transdecoder.genome.gff3

that you can specify to EVM as evidence type "OTHER_PREDICTION"

and hopefully that will work exceptionally well.


The older terminal exon thing has been deprecated in favor of the above
approach, but the above approach hasn't yet made it into the EVM
documentation.
If you could report back on your experience with this, that would be very
helpful.

Please be sure to use the latest PASA as well as the latest EVM software
for best performance.

Good luck!

~brian


On Fri, Aug 30, 2013 at 4:26 PM, de Man, Tom <tom...@em...> wrote:

>  Hi,
>
>  I'm wondering how to include my PASA assemblies into EVM. I'm asking
> because I don't see a parameter in the partition_EVM_inputs.pl script or
> write_EVM_commands.pl but it can be included in the weights file. Or is the
> terminalExons parameter the one I'm looking for? not sure about that. For
> now I removed the PASA_transcript_assemblies line from the weights file and
> used the protein, transcript alignment files and the de novo gene
> prediction GFF only. My data comes from a MAKER run.
>
>  Thanks for your help,
> Tom de Man
>
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-- 
--
Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas