Question: Re: [Galaxy-Dev] Tophat Output
0
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Jianpeng,
The numbers 87 and 93 are the actual maximum lengths of the aligned
regions on either side of the junction. If you want to examine your
pair-end data statistically, the "NGS: Picard (beta)" tool group has
several tool options.
However, examining the track at the gene/transcript level for a few
well
characterized gene bounds is really the best way to understand how the
file describes the data. A browser with your tracks loaded (Trackster
or
UCSC), the text data files, and the Cufflinks manual/FAQ will likely
address most of your questions or at least will be a good orientation.
The visual portion of this helps a great deal.
http://cufflinks.cbcb.umd.edu/faq.html
To address the visualization at UCSC, I can point you to their User
Guide: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html and
contact mailing list: http://genome.ucsc.edu/contacts.html
Good luck with your project. Please remember to keep questions to the
Galaxy team on our mailing lists so that our entire team and community
can contribute/benefit,
Thanks!
Jen
Galaxy team
Subject: RE: [galaxy-dev] Tophat output
Date: Wed, 18 Apr 2012 15:23:43 +0000
To: Jennifer Jackson <jen@bx.psu.edu>
Hi Jennifer,
In the history, I have the splice junction file, and click it to show
the display at UCSC main. Then I click display at UCSC main. It will
open the USCS Genome Browser. Since this is the first time for me to
visualize the splice junction, can you give me more instructions on
how
to visualize it with UCSC genome browser ?
Thanks,
Jianpeng
--
Jennifer Jackson
http://galaxyproject.org