Tophat v1.1 with GTF files

[hyjkim]

I wanted to try tophat 1.1 with a UCSC supplied GTF file, but the binary (linux-x86_64) I downloaded keeps asking for a GFF file. Has anyone had success running this version with a GTF file?

[Thomas Doktor]

I have had succes with the 1.1.0 binary. Are you sure you are running the updated TopHat and not an old one left on your system? You can check using the --version option when you run TopHat ($ tophat --version).

[hyjkim]

It's working! I had some deprecated paths in my scripts which were causing the problem. Thanks for your help!

[Pejman]

where can I get reliable GTF annotation files?

I'm trying to get the GTF files for hg18, preferably at isoform level, from UCSC browser portal, in order to run with Tophat and cufflinks, but apparently I can't find such files there.
So far I've managed to download a table from here http://genome.ucsc.edu/cgi-bin/hgTables?command=start but I'm not quite sure if it's the right way to do it. How did you guys get the file?

thanks

[Thomas Doktor]

You are correct in using the table browser. To download a GTF file of a track, you need to select GTF in the output format dropdown menu, type a name for the output file, for instance hg18.UCSCknowngene.isoforms.gtf, then click get output. That should get you a GTF file.

[Pejman]

yes that what I did, but the problem is that there are loads of options for group/track/table and I don't find any single combination to look significantly more appealing. I'm looking for a detailed annotation for hg18, currently I have taken, the GTF file with:

Group: Genes and Gene prediction Tracks
Track: RefSeq Genes
Table: refGene

but I dunno how sensible/standard choice it is! and I guess it does not contain isoform level annotation.

[krobison]

RefSeq gene does include a lot of isoforms (any that have RefSeq mRNA entries), but there are certainly isoforms expected to be missing.

[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?