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.
I agree with all the excellent answers below. But, I was just curious. Which species of yeast are your working with? Apparently only a small percentage (3-4%) of S. cerivisiae genes are spliced. That could explain why you were "getting away" with a non-splice-aware aligner like bwa. Probably still want to interrogate those spliced genes with an aligner like tophat though. :-)
I was working with Candida parapsilosis. I went with Tophat in the end cause I wanted to be aware of the possible exon/intron junctions.