[carmeyeii]

So you can supply TopHat with a GTF file of annotated transcripts, which, using the --GTF option, will be the first place where reads are mapped, followed by the whole genome, with or without novel junction discovery in this second stage. As I understand it, this is after TopHat 1.4.
I'm curious to know how t was before 1.4. I think you could already give TopHat a GTF file, but it used it second. Am I right? If so, what is the difference between using it [the GTF file] first and using it second after the genome?

Carmen

[gringer]

I'm curious to know how it was before 1.4

I'm not sure about version numbers, but tophat's previous approach didn't try mapping to a transcriptome first. The current approach assembles a transcriptome from the GTF file and maps to that first, then does the novel junction discovery after that on the substantially smaller remainder of reads.

The previous approach was slower (and possibly less accurate), because the junction discovery would be done on all reads, rather than just the ones that didn't map to the known transcriptome.

[carmeyeii]

I see, but it could still use a GTF file at some point, right?