Call interactions from HiC

usage: hic_interactions.py [-h] [-j JID] -f HIC --chr CHR [--juicer_commands JUICER_COMMANDS] [-b BED] [--juicer_tools_path JUICER_TOOLS_PATH] [--HICCUPS_parameters HICCUPS_PARAMETERS]
                           [-g GENOME]

optional arguments:
  -h, --help            show this help message and exit
  -j JID, --jid JID     enter a job ID, which is used to make a new directory. Every output will be moved into this folder. (default: hic_interactions_yli11_2021-07-23)
  -f HIC, --hic HIC     .hic file (default: None)
  --chr CHR             which chr to call (default: None)
  --juicer_commands JUICER_COMMANDS
                        juicer_tools commands to call interactions (default: None)
  -b BED, --bed BED     user input bed file to subset interactions (default: None)
  --juicer_tools_path JUICER_TOOLS_PATH
                        juicer_tools_path (default: /home/yli11/HemTools/share/script/jar/juicer_tools_1.13.01.jar)
  --HICCUPS_parameters HICCUPS_PARAMETERS
                        HICCUPS_parameters relaxed (best for now) (default: -r 25000 -k VC_SQRT -f 0.2 -p 2 -i 5 -t 0.02,1.5,1.75,2 -d 20000 --cpu)

Genome Info:
  -g GENOME, --genome GENOME
                        genome version: hg19, hg38, mm9, mm10. Used for homer annotation (default: hg19)

Summary

From .hic file, call interactions using juicer_tools (specifically, HICCUPS), then given a user input bed file, extract all the regions interacted with this bed file.

The current parameter -r 25000 -k VC_SQRT -f 0.2 -p 2 -i 5 -t 0.02,1.5,1.75,2 -d 20000 --cpu, is almost the same as the default parameter used for Medium resolution HiC data: https://github.com/aidenlab/juicer/wiki/HiCCUPS

But I found -k VC_SQRT -f 0.2 tends to give more called interactions.

Current program use the union of 10k, 25k, 50k, and merged called interactions.

Usage

cd /home/yli11/dirs/genome_browser/yli11/Antonio/relaxed_analysis

=cut hic 1

inputFile=input

ncore=1
mem=20000
q=priority

module load conda3

source activate captureC

hic_interactions.py -f ${COL1} -j ${COL2} -g ${COL3} -b ${COL4} --chr X

Input

hic file, a bed file, a specific chr to call interactions (speed consideration)

Output

The final output is homer annotated. {{jobID}}.{{bed file name column, i.e., 4th column}}.annot.tsv

Comments

code @ github.