Hello Tao,

For the Bowtie results, the aligned results may be low because the data is RNA and not DNA. TopHat is generally considered a better choice for RNA since it allows for bridges over splice sites (introns). The full documentation for each program is on each tool's form and/or you can contact the tool authors with scientific questions at tophat.cuffli...@gmail.com.

Also, a tutorial and FAQ are available here:
http://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise
http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq

For visualization, an update that allows the use of a user-specified fasta reference genome is coming out very soon. For now, you can view annotation by creating a custom genome build, but the actual reference will be not included. Use "Visualization -> New Track Browser" and follow the instructions for "Is the build not listed here? Add a Custom Build".

Help for using the tool is available here:
http://galaxyproject.org/Learn/Visualization

As stated before, please email the mailing list directly and not individual team members. Specifically, with a "to" to the mailing list (only) and not including team members as a "to" or "cc" unless ask to do so when sharing private data. Our internal tracking system and public archives rely on this method. Thank you for your future corporation.

Best,

Jen
Galaxy team

On 8/18/11 3:15 PM, Peng, Tao wrote:
Hi jen, I have used BOWTIE to align my RNA-seq reads to HSV2 genome; out
of 35,000,000 lines, only 621 lines left when I chose to have mapped
reads only. How can visualize these aligned reads to HSV-2 genome?

In the panel of converted SAM to BAM, I tried to use the data in
trickster, but I am not sure to how to build a HSV genome as a
reference?

I appreciate your help,


tao


--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
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