tanlabcode/gmap repository overview

GMAP is an algorithm to call topologically associating domains (TAD) and subdomains (subTAD) from Hi-C data. It is implemented as a R package rGMAP.

⁠Input

• An 3-columns tab delimited hic data file (bin_i bin_j count):

10	11	1.15
10	15	1.89
15	20	2.20
......

• A 4-columns tab delimited index file for hic bin (chromosome start end bin_id) in 10kb resolution:

  chr1	0	10000	1
  chr1	10000	20000	2
  chr1	20000	30000	3
  ......
  

  Copy

• RESOLUTION: resolution of hic bin, default 40000

• Other optional parameters for rGMAP (see following usage example)

⁠Run in Docker

• Install docker

• Put both input hic_file and index_file in current directory, and run the following command:

• docker run -v "$PWD":/home/rgmap tanlabcode/gmap:firstpush Rscript --vanilla /home/rgmap/test_rgmap.R -p YOUR_HIC_FILE_NAME -i YOUR_HIC_BIN_INDEX_FILE_NAME -r YOUR_HIC_DATA_RESOLUTION -m 20 -M 100 -d 2

⁠Output

The identified tads and sub-tads were saved in your current directory named "tads_withLevel.txt"

⁠Reference

The detailed information of GMAP algorithm is described in the following paper:

Yu, W., He, B., & Tan, K. (2017). Identifying topologically associating domains and subdomains by Gaussian Mixture model And Proportion test. Nature Communications, 8, 535.