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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
Attachments:
- image001.jpg (image/jpeg — 19.3 KB)
- attachment.htm (text/html — 3.6 KB)
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
On 7/31/10 11:26 AM, Rehman, Atteeq (NIH/NIDCD) [F] 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?
Untitled-1
*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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Jennifer Jackson
http://usegalaxy.org
4567
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galaxy-user@lists.galaxyproject.org
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Rehman, Atteeq (NIH/NIDCD) [F]