EVM and BRAKER gene prediction

[Alessandro de Mello Varani]

Hi there,

I would like to run EVM with PASA transcripts alignments and BRAKER gene prediction.

I had used BRAKER with RNAseq and Proteins alignments, predicting about 30k genes, and default PASA pipeline parameters.

However, after running EVM, the final results removed a lot of gene predictions.

For instance, after EVM the number of genes drops to 25k.

This seems to be not a reliable results, since I expect in this genome ~29-30 genes

How can I input BRAKER correctly in EVM ? 

Best regards

[Brian Haas]

Hi,

Note, EVM is meant to tackle a set of gene predictions, which means folding in Braker results along with a variety of other ab initio prediction types.  If you're just giving it Braker predictions along with alignment data, it's unlikely to do much. EVM should leverage at least a few different ab initio types.

Be sure to study the EVM paper and the EVM included sample data for more useful info.

best,

~b

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