# Dense mark activity matrices (3.5M+ DHSs x 833 biosamples) in hdf5 format. Loadable with h5py in Python or rhdf5 in R.
# Manifest:
## Rows and columns:
masterlist_DHSs_733samples_WM20180608_all_coords_hg19_epimap_annotated.tsv
masterlist_DHSs_733samples_WM20180608_all_chunkIDs2indexIDs.txt
masterlist_DHSs_733samples_WM20180608_all_coords_hg19_r25_e100_names.core.srt.tsv
masterlist_DHSs_733samples_WM20180608_all_coords_hg19.core.srt.txt
mark_matrix_names.txt
mnemonic_mapping.tsv

## HDF5 Files:
H3K4me2_all_bin_dense_on_mixed_impobs_r25_e100_allchr_merged.hdf5
H3K4me3_all_bin_dense_on_mixed_impobs_r25_e100_allchr_merged.hdf5
H3K9ac_all_bin_dense_on_mixed_impobs_r25_e100_allchr_merged.hdf5
H3K4me1_all_bin_dense_on_mixed_impobs_r25_e100_allchr_merged.hdf5
H3K27ac_all_bin_dense_on_mixed_impobs_r25_e100_allchr_merged.hdf5
DNase-seq_all_bin_dense_on_mixed_impobs_r25_e100_allchr_merged.hdf5
Enhancer_H3K27ac_intersect_matrix.hdf5

# Enhancer/Promoter matrices and indices:
Enhancer_H3K27ac_intersect_matrix.mtx.gz
Promoter_H3K27ac_intersect_matrix.mtx.gz
Promoter_H3K27ac_intersect_matrix.names.tsv
Enhancer_H3K27ac_intersect_matrix.names.tsv
DYADIC_masterlist_indices_0indexed.tsv
PROM_masterlist_indices_0indexed.tsv
ENH_masterlist_indices_0indexed.tsv
PROM_masterlist_locations.bed
ENH_masterlist_locations.bed
DYADIC_masterlist_locations.bed


# File descriptions:
*_all_bin_dense_on_mixed_impobs_r25_e100_allchr_merged.hdf5
- Dense HDF5 matrix with dimensions 3.5M+ (DHSs) by 833 (biosamples)
- Matrix of the average bedgraph signal in the 200bp region centered on the DHS midpoint

mark_matrix_names.txt
- Column names (biosamples) for the HDF5 matrices

mnemonic_mapping.tsv
- Mapping from biosample ids to mnemonics for each of the 833 samples

masterlist_DHSs_733samples_WM20180608_all_coords_hg19_epimap_annotated.tsv
- Overall table of DNase Hypersensitive Sites, locations, row (for slicing hdf5), and names
- DHS masterlist at: http://www.meuleman.org/project/dhsindex/
- Columns: chr start end row name id is.enh is.prom is.dyadic strand
- NOTE: This is a merged version of the three files below, and is preferable to use over those:

masterlist_DHSs_733samples_WM20180608_all_coords_hg19.core.srt.txt
- DNase Hypersensitive Sites (rows) names and locations for HDF5 matrices
- DHS masterlist at: http://www.meuleman.org/project/dhsindex/
- Columns: chr start end old_identifier
- NOTE: Not sorted according to the HDF5 matrix order

masterlist_DHSs_733samples_WM20180608_all_coords_hg19_r25_e100_names.core.srt.tsv
- DNase Hypersensitive Sites (rows) names and locations for HDF5 matrices
- DHS masterlist at: http://www.meuleman.org/project/dhsindex/
- Columns: chr row old_identifier
- NOTE: Sorted according to the HDF5 matrix order

masterlist_DHSs_733samples_WM20180608_all_chunkIDs2indexIDs.txt
- Mapping between chunk names and DHS IDs as in DHS masterlist (at http://www.meuleman.org/project/dhsindex/)
- Columns: DHSid old_identifier

Promoter_H3K27ac_intersect_matrix.hdf5
- HDF5 matrix with dimensions 3.5M+ (DHSs) by 833 (biosamples)
- Sparse matrix of intersection of promoters (ChromHMM) in DHSs with high H3K27ac signal in the 200bp region centered on the DHS midpoint
- Promoter states used in the 18-state model: 1,2,3,4,14

Promoter_H3K27ac_intersect_matrix.mtx.gz
- Above hdf5 matrix in MatrixMarket format (https://math.nist.gov/MatrixMarket/formats.html)

Promoter_H3K27ac_intersect_matrix.names.tsv
- Names of epigenomes (columns) in above matrix

Enhancer_H3K27ac_intersect_matrix.hdf5
- HDF5 matrix with dimensions 3.5M+ (DHSs) by 833 (biosamples)
- Sparse matrix of intersection of enhancers (ChromHMM) in DHSs with high H3K27ac signal in the 200bp region centered on the DHS midpoint
- Enhancer states used in the 18-state model: 7,8,9,10,11,15

Enhancer_H3K27ac_intersect_matrix.mtx.gz
- Above hdf5 matrix in MatrixMarket format (https://math.nist.gov/MatrixMarket/formats.html)

Enhancer_H3K27ac_intersect_matrix.names.tsv
- Names of epigenomes (columns) in above matrix

PROM_masterlist_indices_0indexed.tsv
ENH_masterlist_indices_0indexed.tsv
DYADIC_masterlist_indices_0indexed.tsv
- DHS indexes corresponding to promoter, enhancer, and dyadic elements
- 0-indexed, add 1 to indices for use in R and Matlab, keep as is for Python and similar

PROM_masterlist_locations.bed
ENH_masterlist_locations.bed
DYADIC_masterlist_locations.bed
- All DHS locations for promoter, enhancer, and dyadic elements
- Slices of masterlist_DHSs_733samples_WM20180608_all_coords_hg19_r25_e100_names.core.srt.tsv with locations added