hicmaptools: a command line tool to access HiC maps.
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)
Documentation
Important Notes
- 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
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
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 ~]$