Jen, thank you for following up on my question.
Is any tool in GALAXY to visualize the coverage of aligned reads from
TopHat on human chromosomes (histogram or density plot)?
From: Jennifer Jackson [mailto:email@example.com]
Sent: Thursday, September 15, 2011 2:37 PM
Cc: Peng, Tao
Subject: Re: [galaxy-user] run tophat in galaxy
===> Please use "Reply All" when responding to this email! <===
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
On 9/15/11 1:38 PM, Jennifer Jackson wrote:
===> Please use "Reply All" when responding to this
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
asking a question. Send all questions directly "to"
"galaxy-user(a)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
the GTF file from your history is on the tool's form. If you
questions about the tools that are not addressed by these help links:
then contacting the tool authors would be the next step:
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
Hopefully this helps,
-------- Original Message --------
Subject: run tophat in galaxy
Date: Sun, 28 Aug 2011 08:50:04 -0700
From: Peng, Tao <tpeng(a)fhcrc.org>
To: Jennifer Jackson <jen(a)bx.psu.edu>, galaxy-user
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.
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