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Question: Can I Call Snps And Indels In Galaxy
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gravatar for Mathew Bunj
6.3 years ago by
Mathew Bunj • 100
Mathew Bunj • 100 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
galaxy • 1.2k views
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modified 6.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.3 years ago by Mathew Bunj • 100
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gravatar for Jennifer Hillman Jackson
6.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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 -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k
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