Specificity of augustus
Posted: Thu Nov 19, 2015 5:18 pm
Originally posted in the old forum by Song on 04.04.2014 - 09:40
Hi,
I am try to retraining augustus with RNA-seq data.
Firstly, I took the TAIR10 annotation itself as trianing dataset, and then predict the gene structure of Arabidopsis col. And got a result 1.
Secondly, I used the PASA pipeline to generate a dataset with RNA-seq as training data. And predict the gene structure of Arabidopsis col. Got a result 2.
And found the specificity(true positive/predicted positive) in transcript level of both results are about 60%. So I think the training dataset is good enough, is it correct?
But he specificity(60%) is still far from enough. So I am wondering what's the general value of specificity. And how could I improve it.
Hi,
I am try to retraining augustus with RNA-seq data.
Firstly, I took the TAIR10 annotation itself as trianing dataset, and then predict the gene structure of Arabidopsis col. And got a result 1.
Secondly, I used the PASA pipeline to generate a dataset with RNA-seq as training data. And predict the gene structure of Arabidopsis col. Got a result 2.
And found the specificity(true positive/predicted positive) in transcript level of both results are about 60%. So I think the training dataset is good enough, is it correct?
But he specificity(60%) is still far from enough. So I am wondering what's the general value of specificity. And how could I improve it.