From fa0fc0125bc71d53ff879904e113000585506758 Mon Sep 17 00:00:00 2001 From: Graham McVicker Date: Mon, 25 Apr 2016 18:59:52 -0700 Subject: [PATCH] Update README.md --- CHT/README.md | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/CHT/README.md b/CHT/README.md index b154708..03c6b68 100644 --- a/CHT/README.md +++ b/CHT/README.md @@ -166,9 +166,16 @@ For example, if the goal is to identify histone-mark QTLs, the target regions should be ChIP-seq peaks, and the test SNPs should be SNPs that are near-to or within the ChIP-seq peaks. +Note (added 4/25/2016): the target regions for a single test regions should be +non-overlapping. Overlapping target regions can cause some reads +to be counted multiple times in a single test and inflate the test +statistic. We plan to add a check for this to the extract haplotype +read counts. + If the goal is to identify eQTLs, the target regions should be the exons of genes, and the test SNPs could be SNPs within a specified -distance of the TSS. +distance of the TSS. If a gene contains overlapping or duplicate +exons these should be collapsed. We provide a script, `get_target_regions.py`, that can generate a list of target regions and test SNPs for ChIP-seq peaks that match