Hi
I am trying to determine strand orientation for SNPs using the output from
"http://genome.ucsc.edu/cgi-bin/hgTables"; (all SNPs(135)).
This is in order to impute using 1000 genomes data which requires you to know
the strand orientation of the data. I want to be sure that I fully understand
this table and I am getting the information I need.
In the attached file (exported from tables/SNPs) I have highlighted 4 columns.
Does the "Strand" column refer to the "observed" column. i.e. the observed
column for rs1000073 it is on the "-" strand because it is ("C/T"). For
rs1000073 the "+" strand equivalent is "A" (from refUCSC). Obviously you cannot
use this approach for AT or CG, but I have illumina data and 99% of SNPs are
unambiguous.
Is this correct?
Regards
John
************************************************************************************
John A Curtin
Lecturer in Functional Genomics
Deputy Director, MRes in Translational Medicine
University of Manchester
CIGMR
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