===> Please use "Reply All" when responding to this email! <===
Hi Tao,
I made an error in my prior reply, it is possible to guide assembly in
TopHat. To do this, on the TopHat form, change "TopHat settings to use:"
from "Use Defaults" to "Full parameter list". In the expanded form:
1 - change "Use Own Junctions:" to be "yes".
2 - change "Use Gene Annotation Model:" to be "yes"
3 - in the new pull-down menu, select the GTF file from your history
Great question! Glad that we were able to provide you with the correct
instruction,
Best,
Jen
Galaxy team
On 9/15/11 1:38 PM, Jennifer Jackson wrote:
===> Please use "Reply All" when responding to this email! <===
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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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
