LiMACC is an framework of calling significant interactions from multiple types of chromosome conformation capture assays, including Capture-C, Capture-HiC and HiChIP experiments. It's implemented through a R package limacc.
library(devtools)
install_github("wbaopaul/limacc")
install.packages('path to limacc_1.0.tar.gz', type = 'source', rep = NULL)
chr1 0 3002504 chr1_1
chr1 3002504 3005876 chr1_2
chr1 3005876 3006265 chr1_3
......
- An example of fragment_file (chromosome start end fragment_id) in 5kb resolution for HiChIP is given similarly:
chr1 0 5000 1
chr1 5000 10000 2
chr1 15000 20000 3
......
Note that the fourth column fragment_id could be any user specified character
chr1_10 chr1_11 2
chr1_10 chr1_15 4
chr1_15 chr1_20 5
......
Note that the first two columns in the contact_file should be included in the fourth column of the fragment_file.
library(limacc)
help(limacc)
./limacc4command -f your_fragment_file -c your_contact_file1,file2 -t CHiC
* for more help, see
./limacc4command --help
The detailed information of LiMACC algorithm is described in the following paper:
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