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Tuesday, September 24, 2013

finding the closest feature given a set of Genomic coordinates

I have a bed file which contains peak information for a ChIP-seq data. I want to find the genes that are closest to these peaks.

I am aware that many softwares can do this job. cistrome-Galaxy pipeline from shirley liu's lab in Harvard,  bioconductor package ChIPpeakAnno
are tools can deal with this kind of task. In addition to them, bedtool is a very good tool for Genomic Interval manipulation.  See a post here

However, I want to go a little bit further to learn the Interval Tree data structure to deal with this kind of problem as mentioned in my last post and the post from Biostar.

I will have a look at the bx-python package.

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