Question: Re: [Galaxy-Dev] Tophat Output
gravatar for Jennifer Hillman Jackson
6.6 years ago by
United States
Jennifer Hillman Jackson25k 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. To address the visualization at UCSC, I can point you to their User Guide: and contact mailing list: 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 <> 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
rna-seq cufflinks • 717 views
ADD COMMENTlink written 6.6 years ago by Jennifer Hillman Jackson25k
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