brianjohnhaas
commented
6 years ago Hi Jon,
Nathan Weeks has a fork of PASA that uses sqlite instead of mysql and others have had good success with it. He's in the process of integrating it into the main PASA repo.
I did have plans a while back to fully migrate pasa to the pasa-lite framework, but it lost momentum and I'm not sure if/when I'll get back to it. Trinity sucks up most of my energy these days. ;-)
best,
~b
On Tue, Jan 30, 2018 at 3:32 PM, Jon Palmer notifications@github.com wrote:
Hi Brian,
I'm interested in knowing your plans for PASA lite? I just cloned and tested out the Lite version on some data and it seemed to work okay. I'm interested as it would nice to not have to rely on MySQL as many HPC environments don't let their users use mysql because of security concerns. My main need (or want I guess) is for a way to leverage RNA-seq during genome annotation. IWhat I'm currently doing is to run Trinity, followed by PASA, using those data to train ab initio gene predictors, and then go back and update UTR data using PASA --> this is in my genome annotation package https://github.com/nextgenusfs/funannotate. So I guess an ideal PASA-Lite would also contain a way to compare/update GFF3 annotations using the PASA assemblies.
So it seems like right now PASA Lite could do the assemblies from GMAP/BLAT alignments. For training the gene predictors, running those data then through transdecoder could result in high quality predictions for training. But then currently there would be no way to update gene models with UTRs without using mysql PASA. Are you aware of any other software that does this? Or how much work would it be to convert those scripts to not use mysql?
At any rate, if I can help with anything I'd be more than happy to. My perl skills are not great though....
Best, Jon
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
nextgenusfs
Hi Brian,
I'm interested in knowing your plans for PASA lite? I just cloned and tested out the Lite version on some data and it seemed to work okay. I'm interested as it would nice to not have to rely on MySQL as many HPC environments don't let their users use mysql because of security concerns. My main need (or want I guess) is for a way to leverage RNA-seq during genome annotation. IWhat I'm currently doing is to run Trinity, followed by PASA, using those data to train ab initio gene predictors, and then go back and update UTR data using PASA --> this is in my genome annotation package https://github.com/nextgenusfs/funannotate. So I guess an ideal PASA-Lite would also contain a way to compare/update GFF3 annotations using the PASA assemblies.
So it seems like right now PASA Lite could do the assemblies from GMAP/BLAT alignments. For training the gene predictors, running those data then through transdecoder could result in high quality predictions for training. But then currently there would be no way to update gene models with UTRs without using mysql PASA. Are you aware of any other software that does this? Or how much work would it be to convert those scripts to not use mysql?
At any rate, if I can help with anything I'd be more than happy to. My perl skills are not great though....
Best, Jon