Visualizing loops

Visualization in UCSC / WashU Epigenome Browser

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!)

For WashU Epigenome Browser

We recommend building a WashU track hub to facilitate data i/o and batch visualization. This Rscript may help in creating the .json file for visualization.

Old method of visualizing loops

We’ve publicly distributed an R/Shiny application for visualizing DNA loops called DNAlandscapeR. While DNAlandscapeR is not actively maintained, the latest build is stable and should facilitate visualizing .rds files. The code is all made publicly available here.

To visualize loops in this browser, 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.