Milos Pjanic

4 Questions 8 Answers 0 Followers

Questions related from Milos Pjanic

When is correct to use r2 and when D' for selecting SNPs in LD?

Here is an example. Lets say two SNPs are co-inherited 100% of the times, D' prime will always be 1, while r2 incorporates the information about allele frequencies and thus will be lower than 1 if...

12 December 2016 4,945 6 View

Is there a GTEX trans-eQTL analysis?

Has anyone done a trans-eQTL analysis using data from GTEX? Would it be feasible due to relatively lower sample numbers in GTEX compared to what is required for trans-eQTL data analysis? Thanks

03 March 2016 5,815 1 View

What is the best tool for allele specific chromatin accessibility QTL analysis?

I came across RASQUAL http://www.ncbi.nlm.nih.gov/pubmed/26656845 and WASP http://www.ncbi.nlm.nih.gov/pubmed/26366987 Probably there are more. Is there a comparative analysis of various allele...

01 January 2016 4,416 0 View

How do i compare BWA-aln and BWA-mem aligners?

I am trying to map reads from whole genomes, and considering whether to employ older BWA-aln or newer BWA-mem aligners. BWA-mem will supposedly map more reads than BWA-aln, sometimes this...

12 December 2015 2,416 4 View