Use of several gene predictors

[Juan O A]

Hi,

I'm trying to include as an input output files from SNAP and Augustus, but I cannot see any other way to include both but to duplicate the --gene_predictions parameter, or to run EVM twice, one for each predictor. As I'm having some errors and I haven't seen any examples of those two possibilities, I would like to know whether any of those are possible or not.

Thanks,

[Brian Haas]

Hi,

You would include all the gene predictions in a single input file but set the 2nd column of the gff3 format to indicate the prediction type.  You then identify the gene prediction types in the weights file:

http://evidencemodeler.github.io/

and that prediction type should match the 2nd column value in the gff3 file.

Be sure to look through the example data to examine formatting, etc.

good luck!

~b

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Brian J. Haas
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[Juan O A]

Hi,

Thank you very much for your help. I'll do that then. 

Regards,

El martes, 25 de julio de 2017, 14:47:29 (UTC+2), Brian Haas escribió:

Hi,

You would include all the gene predictions in a single input file but set the 2nd column of the gff3 format to indicate the prediction type.  You then identify the gene prediction types in the weights file:

http://evidencemodeler.github.io/

and that prediction type should match the 2nd column value in the gff3 file.

Be sure to look through the example data to examine formatting, etc.

good luck!

~b

On Tue, Jul 25, 2017 at 3:38 AM, Juan O A <jocho...@gmail.com> wrote:

Hi,

I'm trying to include as an input output files from SNAP and Augustus, but I cannot see any other way to include both but to duplicate the --gene_predictions parameter, or to run EVM twice, one for each predictor. As I'm having some errors and I haven't seen any examples of those two possibilities, I would like to know whether any of those are possible or not.

Thanks,

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[Juan O A]

(I am not sure if the question was sent, so I'll write it again)

Hi again,

There's an error I keep getting in all the partition folders:

error, no chainID in attributes intron_id 2 ; splice_site "TG" of line scaffold1 exonerate:protein2genome:local splice3 33098 33099 . + . intron_id 2 ; splice_site "TG"

 at /home/jotxoteko/soft/EVidenceModeler-1.1.1/EvmUtils/.././evidence_modeler.pl line 1714, <FILE> line 1.

main::parse_evidence_chains('+', 'protein_alignments_exon.gff3') called at /home/jotxoteko/soft/EVidenceModeler-1.1.1/EvmUtils/.././evidence_modeler.pl line 1217

main::load_evidence_data('+', 'protein_alignments_exon.gff3') called at /home/jotxoteko/soft/EVidenceModeler-1.1.1/EvmUtils/.././evidence_modeler.pl line 725

main::process_features('+') called at /home/jotxoteko/soft/EVidenceModeler-1.1.1/EvmUtils/.././evidence_modeler.pl line 385

Always happens with an intron, but I do not really know what chainID info is missing from the column.

Thanks again,

[Brian Haas]

Hi,

best thing to do is to compare your alignment formatting to what's in the example data provided.

best,

~b

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