Changes between Version 4 and Version 5 of SOPs/Hi-C


Ignore:
Timestamp:
11/25/20 11:41:44 (4 years ago)
Author:
twhitfie
Comment:

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  • SOPs/Hi-C

    v4 v5  
    77 * [#SetConfig Set up the HiC-Pro configuration file]
    88 * [#Submit Submit data processing to the LSF batch queue]
     9 * [#ContactMaps Generate contact map visualizations from processed Hi-C data]
    910
    1011=== [=#SetConfig Set up the configuration file] ===
    … …  
    115116}}}
    116117
     118=== [=#ContactMaps Generate contact map visualizations from processed Hi-C data] ===
    117119
     120Hi-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.
     121{{{
     122python2 /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
     123}}}