TopHat juncs file

[seq_GA]

Hi,
How to supply tophat with a list of raw junctions?
Actually I have a set of splice junction set generated using refFlat and Solexa pipeline's splice_sites.pl. How do I convert it to raw-juncs file.

How to generate GFF3 files for human as well as mouse?

[sdriscoll]

building a GFF3 file isn't a very straightforward process. for me it involved doing a bit of work at the command line including installing some Python libraries and downloading code from a CVS repository. you might want to just wait until Tophat supports GTF files which I understand is coming soon. GTF files can be downloaded straight from the UCSC Genome Bioinformatics Table Browser.

[btuser]

Hi,
This post is almost a year old. I am caught in the same situation and was wondering if someone has already written a script to convert refFlat to GFF3 format that I can use here.

[bioinfosm]

I am curious to hear as well...

[lshen]

ucsc_gene2gff.pl

Convert UCSC Genome Browser-format gene files into GFF3 version files.
Only the gene IDs and their locations come through. You have to get
the comments and aliases some other way.

[mrawlins]

It seems that the latest version of TopHat (1.1) allows you to use GTF files, which are more easily obtained. There is at least one other post I've seen detailing how to do that.