Question: No T base in the Illumina report file
0
gravatar for nehal1610.ranabhatt
3 months ago by
nehal1610.ranabhatt0 wrote:

I just extracted the report of the Illumina SNP array genotyping using Illumina genome studio. To be specific, I extracted genotypes of the top strand for each locus. Interestingly, none of the loci displayed Thymine (T) as one of the alleles in a genotype. How can it be possible? Is it because the Illumina defined "Bottom" and "Top" in a certain way where "T" always gets the "bottom" strand designation?

snp illumina array • 179 views
ADD COMMENTlink modified 3 months ago by Istvan Albert ♦♦ 74k • written 3 months ago by nehal1610.ranabhatt0
0
gravatar for Istvan Albert
3 months ago by
Istvan Albert ♦♦ 74k
University Park, USA
Istvan Albert ♦♦ 74k wrote:

Illumina uses a custom SNP designation.

Check the post:

Illumina'S Genome Studio Final Report: Forward Or Top Allele?

and the corresponding document here:

https://www.illumina.com/documents/products/technotes/technote_topbot.pdf

and the blog post:

http://onetipperday.sterding.com/2015/12/snp-allele-coding-schema.html

ADD COMMENTlink written 3 months ago by Istvan Albert ♦♦ 74k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1417 users visited in the last hour