Tuesday, June 24, 2014

Bedtools tutorial from 2013 CSHL course

A couple of months ago I posted about how to visualize exome coverage with bedtools and R. But if you're looking to get a basic handle on genome arithmetic, take a look at Aaron Quinlan's bedtools tutorials from the 2013 CSHL course. The tutorial uses data from the Maurano et al exploration of DnaseI hypersensitivity sites in hundreds of primary tissue types (Science 337:1190-1195).

The tutorial provides examples with pictures and code to do things like:

Intersections to find features that overlap (or do NOT overlap):

Merging features like {ChIP,MEDIP,DNAse,*}-seq peaks:

Examining coverage:

Advanced usage using the Jaccard statistic to measure similarity of all 20 tissue types to all other 20 20 tissues, and visualizing this with principal components analysis and ggplot2 in R:

See the full bedtools documentation for more.

2013 CSHL bedtools tutorial: http://quinlanlab.org/tutorials/bedtools/bedtools.html

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Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License.