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Hello Tao,

The tool "NGS: QC and manipulation -> FastQC" (last tool in group) may be helpful for your project.

In general, sequence with quality scores this low would be considered unusable. Perhaps double check the options used with the Fastq Groomer tool? Or check/filter the data before grooming?

This may not be the case for your data, but just in case, please note that CASAVA 1.8+ now produces both filtered and unfiltered results and would need to be used with the "Sanger" option with the "Fastq Groomer" tool.

This prior Q&A explains the filtering:
http://gmod.827538.n3.nabble.com/Filtering-Illumina-CASAVA-1-8-FASTQ-files-tt3233562.html

Hopefully this helps. Please send future questions directly to the mailing list as the "to" recipient. There is no need to send directly "to" or as "cc" any of the Galaxy team directly. This helps us to track and address questions quickly and as a team.

Best,

Jen
Galaxy team

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: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
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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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
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 http://lists.bx.psu.edu/

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