Configure the parameters for Fast Higashi

All customizable parameters are stored in a JSON config file. The path to this JSON config file will be needed when running the program. For examples of the configuration JSON file, see the tutorials linked in this wiki.

Higashi and Fast-Higashi shares most of the parameters, the JSON file you prepared for Higashi program can be directly reused for Fast-Higashi with a few additional parameters.

Fast-Higashi only parameters

If you plan to run Higashi also, and already prepared the config JSON file according to this, simply include the following parameters, and you are good!

params	Type	Required/Optional	description	example
resolution_fh	list	Required	The resolution of contact maps	[500000]
batch_id	str	Optional	The name of the batch id information stored in label_info.pickle. The corresponding information would be used to remove batch effects	"batch id"
blacklist	str	Optional	Path of the ENCODE black file (https://github.com/Boyle-Lab/Blacklist). Will be used to filter out contacts	"/home/rzhang/Higashi/hg19-blacklist.v2.bed"

Other parameters shared with Higashi

If you plan to only run Fast-Higashi, you will need the following parameters as well.

params	Type	Required/Optional	description	example
data_dir	str	Required	Directory where the data are stored	"/sn-m3C-seq"
input_format	str	Optional	How the data are stored. Can either be "higashi_v1" or "higashi_v2". "higashi_v1" stands for storing the scHi-C dataset as one big table named as data.txt. "higashi_v2" stands for storing contact pairs as individual tables for each cell, and list the path to these files in the filelist.txt	"higashi_v1"
header_included	bool	Required when input_format="higashi_v2"	whether the header of the tab is included in each table	true
contact_header	list	Required when input_format="higashi_v2" and header_included is false	The header of the contact pairs. Must include ["chrom1", "pos1", "chrom2","pos2"], when "count" is not included, the program assumes count=1 for all contact pairs	["chrom1", "pos1", "chrom2", "pos2", "count"]
structured	bool	Required	Whether the data.txt file is structured (interaction pairs of a cell i is successive in the dataframe not randomly placed). If the data.txt is organized before, it could save a lot of memory and time for processing	true
temp_dir	str	Required	Directory where the temporary files will be stored. An empty folder will be created if it doesn't exists.	"../Temp/sn-m3C_1Mb"
genome_reference_path	str	Required	Path of the genome reference file from USCS Genome Browser, will be used to generate bin nodes	"../hg19.chrom.sizes.txt"
chrom_list	str	Required	List of chromosomes to train the model on. The name convention should be the same as the data.txt and the genome_reference file	["chr1", "chr2","chr3","chr4","chr5"]
resolution	int	Required	Resolution for imputation.	1000000
resolution_cell	int	Required	Resolution for generate attributes of the cell nodes. Recommend to use 1Mb (data with lower coverage per cell) or 500Kb (data with higher coverage per cell).	1000000