Anyone have experience with crossing methylation markers (CpGs) with SNPs?
I would like to take a series of methylation markers (CpGs) and match them to a set of GWA SNPs. I have been trying to figure out how to do this kind of thing in PLINK.
There can be several problems on the way: data in different genome builds, finding SNPs either in LD or with effects on CpG sites...
If anyone has done something similar, has resources or instructions, or any particular tips, i'd be interested. Sorry for the n00b question but i'm a doctor, not a bioinformatician :) Live long and prosper!
• 895 views
•
link
written
by
spela.salamon •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
PLINK command --file mydata --r --matrix only generating .ld file
written by KBMP •
-
Controlling for FDR in 450k methylation microarray data
written by eebloom •
-
What are the general strategies in assessing new differentially methylation positions obtained from…
written by samuelandjw •
-
correlation of WGBS dataset and RNAseq dataset
written by frylhc •
-
Finding a SNP in LD with a known SNP (rs number) on a list of SNPs
written by spela.salamon •
-
How to extract proxy SNPs using 1000G vcf for a list of SNPs
written by janhuang.cn
-
Tutorial: Fast LD computation from VCF files using tomahawk
written by firestar
-
Problem in merging 1000G and cases in Plink
written by fatima •
-
Making Linkage Disequilibrium blocks from SNPs position for NCBI Build 38
written by Bahar •
-
basic manipulation of SNP arrays for population genetics
written by platypus998 •
