Genewise

[Tiago Hori]

Hey Brian,

A somewhat related, unrelated question. Do you know if I can use the exonarate gff output instead of genewise? 

I am having a lot of trouble running genewise. 

Thanks!

Tiago

[Brian Haas]

Hi Tiago,

Is this related to EVM instead of PASA?

If you want to use exonerate with EVM, here's the command I used years ago

exonerate --model p2g --showvulgar no --showalignment no --showquerygff no --showtargetgff yes --percent 80 --ryo "AveragePercentIdentity: %pi\n" protein_db.pep target_genome.fasta

and there's a format conversion tool for it here:  EVidenceModeler/EvmUtils/misc/exonerate_gff_to_alignment_gff3.pl

I haven't used this myself in ages - but this is how we used to do it.

If this is really for PASA somehow, let me know and let's discuss it further.

best,

~b

[Tiago Hori]

Hi Brian,

Yes, this is for PASA. I want to add uniref90 mappings, Augustus, MAKER to EVM to use the pipeline described on the PASA website. I want to see how much impacts it has.

Cheers,

Tiago

“If equal affection cannot be, let the more loving one be me” W.H Auden 

On Jul 26, 2021, at 10:17 AM, Brian Haas <bh...@broadinstitute.org> wrote:

Hi Tiago,

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[Brian Haas]

ok, pasa really only uses transcript data (not protein alignments) - unless you're doing the annotation comparison part, in which case it needs a reasonably high quality genome annotation (and not protein alignments) for that part.

EVM will use all those inputs including the pasa alignment assemblies as input, though.

If you're seeing genewise somewhere in the pasa documentation, point me to it because I need to see what's happening there.

best,

~b

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Tiago Hori]

Thanks Brian.

Yes, I want to use EVM with PASA outputs, especially because I ran it with both the gene models and the trinity de-novo assembly. 

The part that talks about genewise in the PASA docs is in here: https://github.com/PASApipeline/PASApipeline/wiki#pasa-in-the-context-of-a-complete-eukaryotic-annotation-pipeline

I am trying to use the complete pipelines described in that section. 

T.

--

"Education is not to be used to promote obscurantism." - Theodonius Dobzhansky.

"Gracias a la vida que me ha dado tanto
Me ha dado el sonido y el abecedario
Con él, las palabras que pienso y declaro
Madre, amigo, hermano
Y luz alumbrando la ruta del alma del que estoy amando

Gracias a la vida que me ha dado tanto
Me ha dado la marcha de mis pies cansados
Con ellos anduve ciudades y charcos
Playas y desiertos, montañas y llanos
Y la casa tuya, tu calle y tu patio"

Violeta Parra - Gracias a la Vida

Tiago S. F. Hori. PhD.
Ocean Science Center-Memorial University of Newfoundland

[Brian Haas]

Gotcha.  Yes, that's all for generating EVM predictions that eventually get fed back into PASA for UTR and alt splice updates.

Exonerate should be fine.  Back in the day, we used a tool called AAT  (which was one of my favorites) for protein alignments. It's kinda slow, but was very powerful.

http://aatpackage.sourceforge.net/

another thing I haven't used in ages given I don't do this kind of work much anymore, but was hugely useful when I did.

best,

~b

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