UTR training sensitivity not improving
Posted: Thu Nov 19, 2015 2:20 pm
Originally posted by PeterM in the old forum on 14.02.2014 - 15:30
Hi everyone,
I am using optimize_augustus.pl (Augustus V2.7) to train parameters. The option --UTR=on was set. For training I use 1000 manually curated genes with UTR.
I am surprised to see that on a test set the sensitivity of the UTRs after training is always worse than to the pre-computed A. thaliana parameters.
The specifictiy however did improved. For testing I always run augustus with "--UTR=on".
Also surprisingly there was no difference when running optimize_augustus.pl with or without the option "--UTR=on".
If I ran optimize_augustus.pl with "--UTR=on --trainOnlyUtr=1" I got an error message.
IntronModel::readProbabilities: Error reading file Tr1_intron_probs.pbl
..Could not read the accuracy values out of predictions.txt when processing bucket 1. at optimize_augustus.pl line 795.
How can I improve the UTR sensitivity?
Is "--UTR=on" set per default or why there is no difference between setting it or not in optimize_augustus.pl.
Many thanks,
PeterM
Hi everyone,
I am using optimize_augustus.pl (Augustus V2.7) to train parameters. The option --UTR=on was set. For training I use 1000 manually curated genes with UTR.
I am surprised to see that on a test set the sensitivity of the UTRs after training is always worse than to the pre-computed A. thaliana parameters.
The specifictiy however did improved. For testing I always run augustus with "--UTR=on".
Also surprisingly there was no difference when running optimize_augustus.pl with or without the option "--UTR=on".
If I ran optimize_augustus.pl with "--UTR=on --trainOnlyUtr=1" I got an error message.
IntronModel::readProbabilities: Error reading file Tr1_intron_probs.pbl
..Could not read the accuracy values out of predictions.txt when processing bucket 1. at optimize_augustus.pl line 795.
How can I improve the UTR sensitivity?
Is "--UTR=on" set per default or why there is no difference between setting it or not in optimize_augustus.pl.
Many thanks,
PeterM