Changes between Version 5 and Version 6 of SOPs/Hi-C

Timestamp:

11/25/20 14:17:00 (4 years ago)

Author:

twhitfie

Comment:

--

SOPs/Hi-C

@@ -120 +120 @@
 Hi-C experiments enable the visualization of chromatin contact maps.  Output from HiC-Pro can be translated into contact maps using [[http://bioconductor.org/packages/release/bioc/html/HiTC.html | HiTC]], the [[https://www.aidenlab.org/juicebox/ | juicebox viewer]] or [[https://github.com/kcakdemir/HiCPlotter | HiCPlotter ]].  To use the juicebox viewer, the HiC-Pro output must first be processed using /usr/local/HiC-Pro_2.11.1/bin/utils/hicpro2juicebox.sh.  The example below illustrates how to use HiCPlotter to visualize the contact map for the Y chromosome using a 100 kb resolution and naming the graphical output file with a "cellType" prefix.
 {{{
-python2 /path/to/HiCPlotter.py -f /path/to/hic_results/matrix/sample1/iced/100000/sample1_100000_iced.matrix -chr chrY -o cellType -n " " -r 100000 -tri 1 -bed /path/to/hic_results/matrix/sample1/raw/100000/sample1_100000_abs.bed -mm 6
+python2 /usr/local/bin/python2.7/HiCPlotter.py -f /path/to/hic_results/matrix/sample1/iced/100000/sample1_100000_iced.matrix -chr chrY -o cellType -n " " -r 100000 -tri 1 -bed /path/to/hic_results/matrix/sample1/raw/100000/sample1_100000_abs.bed -mm 6
 }}}