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Hi Jen, I have been using the following link for learning to visualize TOPHAT 


How can get the RefGENE for the whole human genome instead of Ch19 listed in 



-----Original Message-----
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Thu 8/18/2011 3:46 PM
To: galaxy-u...@bx.psu.edu
Cc: Peng, Tao
Subject: visualization of alignment
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 

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 

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
> reference?
> I appreciate your help,
> tao

Jennifer Jackson

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