The directory contains the following contents which can be used as input to ChromImpute based on the full compendium of data assembled by the Roadmap Epigenomics consortium

*CONVERTEDDATA - this is the directory containing the compendium of data assembled by the Roadmap Epigenomics data already in a converted form that can be used in ChromImpute without 
the need to apply the Convert command except for DNA methylation
*DNAMETHYLDATA - this is the directory containing the DNA methylation input

*hg19sizes_noY.txt - A chromosome info file. In this case containing the lengths of chr1-22 and chrX in hg19. 

These are various input info files:
*tier1_samplemarktable.txt - An input info file restricted to the tier 1 marks: H3K4me1, H3K4me3, H3K27me3, H3K36me3, H3K9me3, H3K9ac, H3K27ac, DNase.
*tier1_tier2_samplemarktable.txt - An input info file restricted to the tier 1 marks (listed above) and the tier 2 marks: H3K4me2, H4K20me1, H2A.Z, H3K79me2
*tier1_tier2_tier3_samplemarktable.txt - An input info file for the tier 1 and 2 marks and the tier 3 marks: H2AK5ac, H2AK9ac, H2BK120ac, H2BK12ac, H2BK15ac, H2BK20ac, H2BK5ac, 
H3K14ac, 
H3K18ac, H3K23ac, H3K23me2, H3K4ac, H3K56ac, H3K79me1, H3K9me1, H3T11ph, H4K12ac, H4K5ac, H4K8ac, H4K91ac
*RNAseq_tier1_samplemarktable.txt - An input info file restricted to the tier 1 marks and RNA-seq. This can be used if trying to predict RNA-seq, but not use RNA-seq to predict other 
marks 


*DNAMethylfiles.txt - this is the info file for imputing DNA methylation when giving the -dnamethyl option
*header_DNAMethyl.txt - the header information file for the DNA methylation

*DISTANCEDIR - this contains precomputed global distances by running the ComputeGlobalDist command on all the tier 1-3 marks

EIDlegend.txt - contains a mapping from EIDs to cell/tissue names