DB: mm9

[mdozmorov]

Our primary focus is hg19-oriented database, so we first need to expand on Cistrome (Issue #10) and FANTOM5 (issue #80) data.

But adding mm9 is a BIG plus, allowing to make a statement "multi-organism support". We need a separate dbcreator that can process http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/

[mdozmorov]

Histone/Source/Cell

• http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechHist/ *.narrowPeak.gz, prefix - "wgEncodeCaltechHist", followed by cell "C2c12", followed by factor "Ab2621". Source - "Caltech"
• http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrHistone/ *.broadPeak.gz, prefix "wgEncodeLicrHistone", followed by cell "Bce, Bmarrow", followed by factor "Input, H3K04me2". Source - "Licr"
• http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuHistone/ *.broadPeak.gz, prefix "wgEncodePsuHistone", followed by cell "Ch12, Erythrobl", followed by factor "H3K04me3". Source - Psu Two exceptions for this data: 1) If file name contains "InputPk", do not process it. 2) Each factor has two replicates. If file name contains "PeaksRep1"/"PeaksRep2", add "rep1"/"rep2" to factor name.

[mdozmorov]

TFBS/Source/Cell

• http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCaltechTfbs/ *.narrowPeak, prefix - "wgEncodeCaltechTfbs", followed by cell, factor. Source "Caltech". Exception: Each factor has two replicates. If file name contains "PkRep1"/"PkRep2", add "rep1"/"rep2" to factor name.
• http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeLicrTfbs/ *.broadPeak.gz, prefix - "wgEncodeLicrTfbs", followed by cell, factor. Source "Licr"
• http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/ *.broadPeak.gz, prefix - "wgEncodePsuTfbs", followed by cell, factor. Source "Psu". Two exceptions for this data: 1) If file name contains "InputPk", do not process it. 2) Each factor has two replicates. If file name contains "PeaksRep1"/"PeaksRep2", add "rep1"/"rep2" to factor name.
• http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/ *.narrowPeak.gz, prefix - "wgEncodeSydhTfbs", followed by cell, factor. Source "Sydh"

[mdozmorov]

DNase/Source/Cell

• http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDnase/ *.broadPeak.gz. Prefix - "wgEncodeUwDnase", everything before "Hotspot" is cell, "DNase" - factor. Source "Uwdnase". Exception: cut "RepXX" from the file name, where XX may be 1, 2, V2, 3, 4, 5, etc., and attach to factor name.
• http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeUwDgf/ *.broadPeak.gz. Prefix - "wgEncodeUwDgf", everything before "Hotspot" is cell, "Dgf" - factor, source - "Uwdgf"
• http://hgdownload.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuDnase/ *.narrowPeak.gz. Prefix - "wgEncodePsuDnase", everything before "Pk" is cell, "DNase" - factor. Source - "Psu"

[mdozmorov]

When adding "rep1"/"rep2", use underscore "". This will make it consistent with our convention of separating Cell-Factor-Source with dashes, but additions with "", e.g. "E067-DNase_bPk-processed".

For Histones and TFBSs, use corresponding source name verbatim. E.g., "Ch12-Cjun-Tfbs" should be "Ch12-Cjun-Sydh"