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hicmaptools is a command line tool to access HiC maps. The complete program provides multi-query modes and analysis tools.

References:

• Jia-Ming Chang, Yi-Fu Weng, Wei-Ting Chang, Fu-An Lin & Giacomo Cavalli
  HiCmapTools: a tool to access HiC contact maps
  BMC Bioinformatics volume 23, Article number: 64 (2022)

• hicmaptools Github page
• hicmaptools Documentation

• Module Name: hicmaptools (see the modules page for more information)
  
• Unusual environment variables set
  • HICMAPTOOLS_HOME  installation directory
  • HICMAPTOOLS_BIN  executable directory
  • HICMAPTOOLS_DATA  sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
[user@cn3144 ~]$ module load hicmaptools
[+] Loading singularity  3.10.5  on cn3144
[+] Loading hicmaptools  20230303

The basdic usage of the hicmaptools application is as follows:

[user@cn3144 ~]$ sinteractive
[user@cn3144 ~]$ hicmaptools -h
hicmaptools -in_map in.binmap -in_bin in.bins QUERY_MODE query.bed -output out_file.tsv
or
hicmaptools -in_hic in.hic [-in_hic_norm NONE] [-in_hic_resol 10000] QUERY_MODE query.bed -output out_file.tsv
or
hicmaptools -in_gin in.gin QUERY_MODE query.bed -output out_file.tsv

input:
        -in_map        text .n_contact or binary .binmap by genBinMap command
        -in_bin        the bin file for contact map, .bins
        or
        -in_hic        .hic file generated by Juicer
        -in_hic_norm   optional, a normalization method (NONE|VC|VC_SQRT|KR, default: NONE)
        -in_hic_resol  optional, a resolution used to bin .hic (default: 10000)
        or
        -in_gin        .gin file in ginteractions format

QUERY_MODE:
        -bait           calculate average contacts from downstream to upstream of interested position

        -local         list all contacts inside an interval

        -loop          contact intensity between two ends of a loop

        -pair          contacts between a pair region

        -sites         contacts between sites

        -submap        sub contact map of interested regions

        -TAD           sum and average of contacts inside TAD region

other parameters:
        -ner_bin       check neighbouring bins for bait mode, (default: 10)
        -random        the size of the shuffle sample, you can turn off shuffle test by 0 (default: 100)
[user@cn3144 ~]$ cp $HICMAPTOOLS_DATA/* .
[user@cn3144 ~]$ hicmaptools -in_map fly_30k.binmap -in_bin fly_30k.cbins -bait bait.bed -o utput temp.tsv
Input
         map   =        fly_30k.binmap
         bin   =        fly_30k.cbins
         query =        bait.bed
Parameters
         ner_bin     =  10
         random size =  100
Output
         output =       temp.tsv

[BEGIN]
        reading contact file =  fly_30k.binmap
        map size             =  3144718

        reading index file =    fly_30k.cbins
        reading # of chrs  = 6
        reading # of bins  = 3985

        reading BAT file =      bait.bed
                # of BATs =     1

        generate random for 20 20       random size = 100 ... [DONE]

[END]

End the interactive session:

[user@cn3111 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$