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:

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:

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.


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

I appreciate your help,


Jennifer Jackson
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