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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
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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:
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 links
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. RefSeq?