augustus training and prediction from scratch
Posted: Wed Nov 18, 2015 6:38 pm
Originally posted by Cecilia in the old forum on 23.05.2012 - 21:59
I've got genome.fa, some EST sequences and RNA-Seq data for a
species. How to do training and genome annotaion using augustus pipeline?
My plan is
* De novo assembly of RNA-seq reads and get transcripts.fasta file
* cat transcripts.fa ESTs.fa > evidence.fa
* autoAug.pl --species=NewSpecies --genome=genome.fa --trainingset=evidence.fa --pasa --cdna=evidence.fa --maxIntronLen=1000
Is there anything wrong with my plan? Should I generate hints from RNASeq and ESTs before running autoAug.pl?
I've got genome.fa, some EST sequences and RNA-Seq data for a
species. How to do training and genome annotaion using augustus pipeline?
My plan is
* De novo assembly of RNA-seq reads and get transcripts.fasta file
* cat transcripts.fa ESTs.fa > evidence.fa
* autoAug.pl --species=NewSpecies --genome=genome.fa --trainingset=evidence.fa --pasa --cdna=evidence.fa --maxIntronLen=1000
Is there anything wrong with my plan? Should I generate hints from RNASeq and ESTs before running autoAug.pl?