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Hello Tao,

Sorry for the delayed reply, your question did not post to the mailing list since the "to" was not _only_ to galaxy-user.

Going forward, please leave off any "to" or "cc" to team members when asking a question. Send all questions directly "to" "galaxy-u...@bx.psu.edu" and do not include any "Re" or "Fwd" text in the subject line.

Regarding RNA-seq analysis and reference GTF files, the place to incorporate the GTF file is in the Cufflinks step, the option to select the GTF file from your history is on the tool's form. If you have questions about the tools that are not addressed by these help links:

http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq
http://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise

then contacting the tool authors would be the next step:
email tophat.cuffli...@gmail.com

To visualize the data, the available options will be links associated with each dataset (expand the dataset box to locate these). The Galaxy Track Browser (GTB) aka "Trackster", UCSC Genome Browser, Ensembl, and GeneTrack are potential options; the datatype will determine which links are provided.

Hopefully this helps,

Best,

Jen
Galaxy team


-------- Original Message --------
Subject:        run tophat in galaxy
Date:   Sun, 28 Aug 2011 08:50:04 -0700
From:   Peng, Tao <tp...@fhcrc.org>
To:     Jennifer Jackson <j...@bx.psu.edu>, galaxy-user
<galaxy-user@lists.bx.psu.edu>



Hi how can I specify a GTF gene annotation file when running tophat to
guide the alignment to human genome? What is the best way to visualize
the tophat results in the context of annotated human genome, i.e. RefSeq?

Thanks,

tao


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