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gravatar for Rehman, Atteeq (NIH/NIDCD) [F]
8.3 years ago by
Rehman, Atteeq (NIH/NIDCD) [F] • 20
Rehman, Atteeq (NIH/NIDCD) [F] • 20 wrote:
Hello, I have a list of variants(SNPs) that differ from reference sequence (in my human subject DNA) and I want to filter out the known variants reported in dbSNP, so that I can have a short list of putative novel variants. Could somebody please tell me how can I do this? [cid:image001.jpg@01CB30BC.5FD96A20] Atteeq Ur Rehman Visiting Fellow National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Room 2A-19, 5 Research court, Rockville, MD, USA, 20850. Lab Ph. No. 301-402-9059
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modified 8.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 8.3 years ago by Rehman, Atteeq (NIH/NIDCD) [F] • 20
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gravatar for Jennifer Hillman Jackson
8.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Atteeq, The general path would be to: 1) get dbSNP data & format 2) upload your own data & format 3) compare Use "Get Data: Bx Main" to obtain dbSNP data. Format using tools in "Text Manipulation" to reduce content to a simple BED (Interval) file. Format your own data to be in a similar form. Then use tools from "Operate on Genomic Intervals: Intersect/Subtract/etc.". Or format so that the dbSNP data form mirrors your own and use "Join, Subtract and Group: Subtract Whole Query" for the comparison. A simplified comparison history with multiple example outputs is here: dbSNP 130 vs dbSNP 131: hg19 chrom 10: http://test.g2.bx.psu.edu/u/jenjackson/h/snp-subtract-example-8-2-2010 More SNP specific tools to explore: NGS: Indel Analysis SNP/WGA:* Thanks, Jen Galaxy Team -- Jennifer Jackson http://usegalaxy.org
ADD COMMENT • link written 8.3 years ago by Jennifer Hillman Jackson ♦ 25k
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