Visualization dataset index correction, please see below:

On 3/7/12 6:56 AM, Jennifer Jackson wrote:
Hello,

I was able to create a visualization using hg19 as the reference and
load this dataset and visualize it.  It is important to allow the BAM
file to index fully, do not navigate away from the page while this is
going on.

I stated this incorrectly. Once a dataset starts indexing, it will complete successfully even if the visualization is saved and/or closed.

As a test, I also used SAMTools BAM-to-SAM, then SAM-to-BAM
(with hg19), to see if there would be any errors (indicating that an
incorrect genome was used), but there were none. This sorted BAM file
also visualized fine.

Once you had the hg19 visualization created, and the BAM file added as a
dataset, there are two key items to change. The first is to set the
chromosome to chr22. The second is to set the display. Hover over the
buttons next to the track name, click on the display options button, and
uncheck the button where only differences are displayed.

For analysis, please see the tools in the groups NGS: Indel Analysis and
SAMTools Mpileup.

On the test server (http://test.g2.bx.psu.edu/) under NGS: Variant
Detection, an unsupported version of FreeBayes is available (with VCF
output).

More about SNP analysis is linked from this page (first set of links
under "Other exercises"): http://main.g2.bx.psu.edu/u/james/p/exercises.

Using the tool search and entering "SNP" as a keyword will locate more
tools. All tool on the main server have help on the tool form and links
to documentation.

Best wishes for your project,

Jen
Galaxy team

On 3/7/12 4:14 AM, DeQuincy Prescott (UCL) wrote:
Test of forward email.

-----------------------------------------------------
DeQuincy Prescott
Sen Res Tech to Professor Bhattacharya
-----------------------------------
about our group
http://tinyurl.com/3264vn
------------------------------------
Mobile: +44 (0) 7590 695 435
Office: +44 (0) 207 608 6951
-----------------------------------------------------

Begin forwarded message:

*From: *"DeQuincy Prescott (UCL)" <smgx...@live.ucl.ac.uk
<mailto:smgx...@live.ucl.ac.uk>>
*Subject: **visualisation of a bam file *
*Date: *6 March 2012 19:03:23 GMT
*To: *<galaxy-u...@bx.psu.edu <mailto:galaxy-u...@bx.psu.edu>>
*Cc: *Jennifer Jackson <j...@bx.psu.edu <mailto:j...@bx.psu.edu>>

One of the concerns I am trying to resolve is that I have a bam file
which I am trying to visualise on galaxy.

http://main.g2.bx.psu.edu/u/dqnc/h/unnamed-history

I was hoping to visualise the data here in Trackster
(http://main.g2.bx.psu.edu/visualization/list)

But it doesn't seem to render.

I have used "Reference genome build (dbkey): Human Feb. 2009
(GRCh37/hg19) (hg19)"
But get "no data for this chrom/contig." as a display message.

The original data is http://qnctv.com/science/chr22hg19.bam (55MB)

Ultimately we would like to be able to get a VCF file or even better
still an essential changes file where known SNPs have been filtered
out and any polymorphism have been checked for possible changes to
amino acid sequence.

I am new to Galaxy and still exploring what it can do so correct me if
it can't perform what I would like it to do.

Thank you for any help you can provide.

-----------------------------------------------------
DeQuincy Prescott
Sen Res Tech to Professor Bhattacharya
-----------------------------------
about our group
http://tinyurl.com/3264vn
------------------------------------
Mobile: +44 (0) 7590 695 435
Office: +44 (0) 207 608 6951
-----------------------------------------------------




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