Bedtools

get the peaks that shared in multiple samples

define intronic, exonic and intergenic regions using GRanges

You might want to use the bedtools for solutions. see Dave Tang’s post.

hosting bigwig by dropbox for UCSC visualization

First, you need to get an idea of what is a bigwig file:

mysql to get all the disease associated SNPs

I want to find SNPs occur at the transcription binding sites which may potentially affect the binding of the transcription factor.

My first play with GRO-seq data, from sam to bedgraph for visualization

GRO-seq (Global run on sequencing) is a technique to capture nascent RNAs in a global manner. Different from RNA-seq which sequences the matured mRNA to…