rna-seq
Posted: Thu Nov 19, 2015 2:24 pm
Originally posted by Assaf in the old forum on 01.05.2013 - 16:40
Hi all,
I see that RNA-Seq supported predictions in augustus become quite accurate by using intron-hints from splice junctions data (similar to what described in http://augustus.gobics.de/binaries/readme.rnaseq.html). The wig hints did not contribute at all in my case.
Still, I see that the program sometimes tends to extend the CDs and exons beyond regions supported by evidence, leading to concatenation adjacent genes, which are not linked by any intron-evidence. I tried to use lower malus values, but this just leads to the increasing this problem ( I expected it will lead to the oposite). Maybe you have an idea how to solve this problem ???
Best,
Assaf
Hi all,
I see that RNA-Seq supported predictions in augustus become quite accurate by using intron-hints from splice junctions data (similar to what described in http://augustus.gobics.de/binaries/readme.rnaseq.html). The wig hints did not contribute at all in my case.
Still, I see that the program sometimes tends to extend the CDs and exons beyond regions supported by evidence, leading to concatenation adjacent genes, which are not linked by any intron-evidence. I tried to use lower malus values, but this just leads to the increasing this problem ( I expected it will lead to the oposite). Maybe you have an idea how to solve this problem ???
Best,
Assaf