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!)