Question: Illumina And Symmetric Snps Problem
1
gravatar for Joey
7.5 years ago by
Joey410
Seattle
Joey410 wrote:

Can someone explain me the issue with Illumina and symmetric SNPs i.e. SNPs with A/T or C/G? I have read quite a few papers which excludes these symmetric SNPs because of strandedness issues.

Thanks,

-Joey

illumina snp strand • 1.6k views
ADD COMMENTlink written 7.5 years ago by Joey410
1
gravatar for Matt Shirley
7.5 years ago by
Matt Shirley9.2k
Cambridge, MA
Matt Shirley9.2k wrote:

See this technical note from Illumina. The basic issue is that Illumina always designates A or T as allele "A", and C or G as allele "B", unless there is an A/T or C/G, in which case the surrounding sequence is evaluated to determine which nucleotide is allele "A" and which is "B".

ADD COMMENTlink written 7.5 years ago by Matt Shirley9.2k
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