Calling Loops

This code snippet shows how to call loops with extract_bedpe in a Docker or Tinker environment. Access the toolkit from our GitHub repository.

First, type list_samples to see what samples are available.

list_samples

Choose a sample to work with. Here, we’ll use GM12878_H3K27ac.

sample=GM12878_H3K27ac

We’ll also define the genome build and range of interest.

genome=hg38
range=chr2:64500000:65000000

To print the loops in your terminal, use:

extract_bedpe --sample1 $sample --genome $genome --range $range --mode loop

To save the loops to a file, use:

extract_bedpe --sample1 $sample --genome $genome --range $range --mode loop > my_loops.bedpe

To visualize these loops, please continue to the next Snippet: Visualizing Loops