Hi everyone !
This will be my first time using Tophat. I'm working on a drosophila genome, and as I read the manual before to start, I saw that there is a little recommendations :
Please note: TopHat has a number of parameters and options, and their default values are tuned for processing mammalian RNA-Seq reads. If you would like to use TopHat for another class of organism, we recommend setting some of the parameters with more strict, conservative values than their defaults. Usually, setting the maximum intron size to 4 or 5 Kb is sufficient to discover most junctions while keeping the number of false positives low.
As Drosophila genomes are very dense in genes, maybe there is an optimal parameters set. Does anyone have an idea of what I should modify to enhance my results ?
PS : The drosophila species I'm working on contains also a high level of polymorphism, so maybe it could be a problem. My main goal is to annotate a assembly I've made of this species. And in order to do that, I have to produces RNA-seq evidences coming from my data. That's why I'm using Tophat at this stage
Thanks for your help !