Visualizing loops

Interactive visualization of loops

One you’ve (hopefully) assessed that your samples look good, now go visualize them! One option is to link the .bedpe file to the WashU Genome Browser. Another option is to upload the .rds to our genome topology browser, DNAlandscapeR. Navigate to the Guide tab to get a sense of how the browser works and ultimately add your sample(s) to a local user session using the Import tab. Note: the browser currently supports hg19/hg37 and mm9 genome builds.

Visualization in UCSC

Users can specify the --make-ucsc flag to produce output that can be imported into UCSC. See this discussion for an overview of the format. In order to produce this output, hichipper needs access to the htslib suite of tools in the computational environment. You can see if you have these dependences available (namely, tabix and bgzip) by making sure the following works:

tabix --version

Specifying this flag will create the additional files *.txt.gz and .txt.gz.tbi, which can be used to make a UCSC track. (Shout out to Gary for helping us with this!)