Hi jen, I followed the GALAXY web cast to check the quality of RNA-seq data: one sample seem to have score above 20 in most bases (R2); but the other one is around 6-8 in most bases (R4) (see the attached PDF files).

Does this mean R4 RNA-seq data are BAD? What exactly does it mean anyway?

Thanks for your help,


tao


-----Original Message-----
From: Jennifer Jackson [mailto:jen@bx.psu.edu]
Sent: Thu 8/18/2011 3:46 PM
To: galaxy-user@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
tophat.cufflinks@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