Contact: Misha Bilenky (mbilenky@gmail.com)

Original file location: ftp://ftp.bcgsc.ca/public/mbilenky/112epigenomes/5mC/ contains SBS, RRBS and mCRF data uniformly processed.

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WGBS data (Whole genome Bisulfite sequencing)
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Original directory location: ftp://ftp.bcgsc.ca/public/mbilenky/112epigenomes/5mC/SBS_Removed_E027_E064_Fixed_E012/

Files:
(1) ReadCoverage.tar.gz : Provides read coverage at CpGs.
Contains 25 files. One for each chromosome.
Format of each file within the tarball : Tab separated table CpGs (rows) X epigenomes (columns)
- The first column is chromosomal position (1-based) of C/G in the CpG
- The rest of the columns are epigenomes. Order of epigenomes is provided in EG.mnemonics file contains the corresponding mnemonics.


(2) FractionMethylation.tar.gz: Provides fractional methylation calls at CpG. 
Contains 25 files. One for each chromosome.
Format of each file within the tarball : Tab separated table CpGs (rows) X epigenomes (columns)
Methylation calls are round to two decimal digits.

Each file has the same matrix format:
- The first column is a position of C or G in the CpG
- The rest of the columns are epigenomes. A file  gives the order. EG.mnemonics file contains the corresponding mnemonics.

Only CpG info is present (as it came from EDACC files); for those CpG where coverage was <=3 we - for both coverage and Methylation (as missing data)

SBS QC information: https://drive.google.com/file/d/0B0FI28XMU8GKLUJyV0ViY3g3eVk/edit?usp=sharing

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RRBS data (Reduced representation Bisulfite sequencing)
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The RRBS matrices are at ftp://ftp.bcgsc.ca/public/mbilenky/112epigenomes/5mC/RRBS/

Folder content
File:EG.mnemonics.name.xls 3 KB 10/26/2012 4:34:00 AM
File:FractionalMethylation.tar.gz 297329 KB 10/26/2012 4:44:00 AM
File:FractionalMethylation.tar.gz.md5sum 1 KB 10/26/2012 4:50:00 AM
File:ReadCoverage.tar.gz 300406 KB 10/26/2012 4:45:00 AM
File:ReadCoverage.tar.gz.md5sum 1 KB 10/26/2012 4:50:00 AM
File:header 1 KB 10/26/2012 4:34:00 AM

1. header gives the order of epigenomes
2. EG.mnemonics.name.xls - tab delimited details
3. Both tars contain 25 matrices per chromosome, each matrix is (52+1) x (number of CpG per chromosome); the locations with no coverage have '-1' value (missing data). ReadCoverage - positive integer number (or -1); FractionalMethylation - 0..1 float number, two decimals (or -1).

RRBS QC information: https://drive.google.com/file/d/0B0FI28XMU8GKbUc3VU12RlBlem8/edit?usp=sharing

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mCRF data
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ftp://ftp.bcgsc.ca/public/mbilenky/112epigenomes/5mC/mCRF_Removed_E060/

File:EG.mnemonics.name.xls 1 KB 10/30/2013 7:17:00 AM
File:FractionalMethylation.tar.gz 383681 KB 10/30/2013 7:51:00 AM
File:FractionalMethylation.tar.gz.md5sum 1 KB 10/30/2013 7:56:00 AM
File:header 1 KB 10/30/2013 7:15:00 AM

There is a tar file with all chromosomes matrices for 17 epigenomes; FractionalMethylation only. CpG values only.

mCRF QC information: https://drive.google.com/file/d/0B0FI28XMU8GKZW5mbHFPOU42c3M/edit?usp=sharing1put headernamed