GATE is a model-based, open source tool for chromatin states prediction based on time-course Epigenetic marks data.

Data File Format

[A script to generate this input file from a list of BED files can be found on Github.]

Specific format for the expression data files is needed to loaded into GATE. All data files should be saved as tab-delimited text files. The first row of the data file consists of descriptions of each column including window location information (chromosome, start, end), and each epigenetic mark in each time point. See "Data.txt" for further information.

Standard data file:

chr	start	end	mark1_time1	mark2_time1	mark3_time1	...	mark1_time2	mark2_time2	mark3_time2	...	...
chr1	6272600	6272799	0.445236	5.143277	1.616379	...	0	3.62483	7.509387	...	...
chr1	7103600	7103799	4.007124	14.69508	8.081897	...	4.962779	9.515179	2.503129	...	...
chr1	7488800	7488999	7.123776	5.143277	2.155172	...	3.158132	18.57725	5.006258	...	...
chr1	9621400	9621599	3.116652	2.939015	2.693966	...	1.804647	11.32759	13.14143	...	...
... ...

 

The data (after 4th column) should be in a order that first list all the marks in one time point and then another time point.

 

Last updated on 07/01/2012 by Pengfei Yu