IDEAS output files included in this directory are:

S3V2_IDEAS_hg38_r3_withHg38Mm10prior.state: The Epigenetic states and position classes for the human (hg38) hematopoietic system. The Joint epigenetic states were used as prior IDEAS epigenetic state.
	First 4 columns are index, chr, position_st position_ed (position_ed will be the same as position_st if only one position for each window is provided in input) 
	The next N columns are epigenetic states, where N=total number of cell types, including replicates. 
	The last column is the position class label in IDEAS local clustering.

S3V2_IDEAS_hg38_r3_withHg38Mm10prior.para.modified.para: Frequency, sum for each of the joint human and mouse epigenetic states in human (hg38) hematopoietic system.
		The first column in the Frequency of the state
		The next N columns are the sum and variance parameters for each epigenetic states.

S3V2_IDEAS_hg38_r3_withHg38Mm10prior.para.modified.para.pdf: The heatmap showing the contributions of the different marks to the states.

S3V2_IDEAS_hg38_ccre2.cCRE.M.notall0.bed: The cCRE list in human (hg38) hematopoietic system identified by S3V2-IDEAS IS module. 

S3V2_IDEAS_hg38_ccre2.cCRE.M.notall0.rmallNEU.bed: The cCRE list in human (hg38) hematopoietic system identified by S3V2-IDEAS IS module, run with the NEU data
removed from the cell specific portion of the run. 
The NEU data is noisy and produced large cCREs. (Sept 2021)

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The files for the tracks associated with this data are available from
https://newbadger.bx.psu.edu/downloads/hg38/bbi/ideasJointMay2021/
The folders here contain:
        NBP: -log10(NB p-value) signal 
        RC: normalized read counts
        ideasJM21ccreSig: Intensity states: the discretized signal intensity levels for ATAC-seq
        meryhg38f8Js26BpSJ: segmentations per cell type using the joint run of IDEAS 
        meryhg38f8s39BpSJ: segmentations per cell type using human only run of IDEAS