Hello Mathew,
The short answer is yes, Galaxy has many tools to do this type of analysis.
If you are new to Galaxy, you will probably want to start in these
places to get acquainted with the UI and tool organization:
https://main.g2.bx.psu.edu/u/james/p/exercises
http://wiki.g2.bx.psu.edu/Learn
http://wiki.g2.bx.psu.edu/Learn/Screencasts
The basic steps are:
0 - Load and Groom your FASTQ data
1 - Map your data (BWA would be a good choice) vs hg18
2 - Select a tool to call novel SNPs/Indels. Click on the "gear icon" at
the top of the left tool panel and enter the keyword "SNP".
3 - Known SNPs: "Shared Data -> Data Libraries". Or, "Get Data -> UCSC
Main" or your other favorite source.
4 - More tools: 'Operate in Genomic Intervals', 'Human Genome
Variation', 'Genome Diversity', NGS: SAM Tools, GATK-beta (genome
"hg_g1k_v37" only).
Hopefully this helps you to get started,
Jen
Galaxy team
On 8/2/12 11:45 AM, Mathew Bunj wrote:
I have two DNA seq files for hg18 and want identify SNPs in each file
as compare dto existing database and also want to find differences (seq
variations) among two samples. I was wondering if I can do that or not
in Galaxy (public server)?
I know I can use liftover to convert into hg19 if need be.
Thanks
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--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
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,
please use the interface at:
http://lists.bx.psu.edu/
