Question: How much overlap to consider when annotating a region
0
gravatar for Saad Khan
5.9 years ago by
Saad Khan400
United States
Saad Khan400 wrote:

Hi I have chip and Dna methylation data in 300bp windows. I am trying to annotated these windows as falling into different kinds of regions e.g. intergenic,exon,intron,utr,promoter etc. I have already fetched this information from gtf file using the method described here http://davetang.org/muse/2013/01/18/defining-genomic-regions/ using bedtools. Now I want to annotate my windows as either falling into either of these regions. I am confused about a few things and would be glad if someone could help me out. 

1. What percentage of overlap should I consider in order to unambiguously divide my tiles into either of the annotation.

2. If I don't consider overlap and only consider regions to be belonging to certain kind of annotation then what parameters can be best used to do it.

ADD COMMENTlink modified 5.7 years ago by PoGibas4.8k • written 5.9 years ago by Saad Khan400
0
gravatar for PoGibas
5.7 years ago by
PoGibas4.8k
Vilnius
PoGibas4.8k wrote:

Simple answer would be: "Are you ready to try some R?!" :-)

See my answer in Overlap between 2 sets of genomic regions of differing size - use GenometriCorr, it will produce reliable results and nice visualisations.

 

 

 

ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by PoGibas4.8k
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