There is a typo somewhere - Histone/Tier1 has "K562b" cell type, should be "K562"
Add 'Monocytescd14ro01746' to Tier2 cell types
DNAse peaks come in different flavors, e.g.
E003-DNase.hotspot.broad.bed.gz
E003-DNase.hotspot.fdr0.01.broad.bed.gz
Right now, they are dumped in one file name, E003-DNase.bed.gz. But there should be different files, with 'hotspot.broad' and 'hostpot.fdr0.01.broad'. There are other postfixes in DNAse data that should be kept.
These histone modifications are downloaded but not processed into "Histone" folder: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwHistone/ http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhHistone/ Update: they are processed, but at later time point.
There is a typo somewhere - Histone/Tier1 has "K562b" cell type, should be "K562"
Add 'Monocytescd14ro01746' to Tier2 cell types
DNAse peaks come in different flavors, e.g. E003-DNase.hotspot.broad.bed.gz
E003-DNase.hotspot.fdr0.01.broad.bed.gz
Right now, they are dumped in one file name, E003-DNase.bed.gz. But there should be different files, with 'hotspot.broad' and 'hostpot.fdr0.01.broad'. There are other postfixes in DNAse data that should be kept.