Hi. This is probably a ridiculous question, but I'm just getting confused the more I read up on it.
Basically, when mapping reads generated by RNA-seq against a genome, is there a specific mapping software you should use? I thought that it was ok to use any of them, like either Tophat, BWA or bowtie, but I was reading other articles and posts that say only Tophat should be used on RNA-seq data. So is this the case?
I should probably point out that my data is single end and strand specific RNA-seq of a yeast species.
I just want to know if I'm doing things right, as I was going to go with BWA as it's given me a slightly higher mapping percentage than Tophat.
Thanks, I really appreciate any pointers you can provide.