# Sept 13, 2010

All three external libraries and all six internal ones (H1 batch 1) have been rerun using BWA against hg18 and FP4.0.15 by Richard + Dorothy.
Original wigs can be found in:
/projects/tab/data/Peaks/SLX-ChIP<libraryid>/FP4.0.15/
with the external library wig files found in:
/projects/tab/data/Peaks/External/126/<libraryid>/FP4.0.15/ (SPADE_FC61JRA,  SUZ12_Rep1, and YY1_Rep1)

Previous files based on sgr and liftover have been moved to: "using_sgr_and_liftover"

# June 2, 2010

1. Run sgrToCustomGFF.py

python ~/bzr-projects/PatternBrowser_gsc_mirror/PatternBrowser-trunk/scripts/sgrToCustomGFF.py UCD370_CtBP2_H1hES_hg19_sgr/UCD370_CtBP2_H1hES_hg19_SOLE_rawbinning.sgr UCD370_CtBP2_H1hES_hg19_customGff/UCD370_CtBP2_H1hES_hg19_SOLE_rawbinning.gff 30

2. Run liftover on this new GFF file

/home/cydneyn/scripts/liftOver -gff UCD370_CtBP2_H1hES_hg19_customGff/UCD370_CtBP2_H1hES_hg19_SOLE_rawbinning.gff /home/cydneyn/scripts/hg19ToHg18.over.chain UCD370_CtBP2_H1hES_hg18_customGff/UCD370_CtBP2_H1hES_hg18_liftover.gff UCD370_CtBP2_H1hES_hg18_customGff/UCD370_CtBP2_H1hES_hg18_liftover.unMapped 

CtBP2:

all:
29,821,031 mapped
    20,545 unMapped
29,841,576 total (<0.1%)

chr10:
1,475,674 mapped
       13 unMapped

Suz12:

all:
66,026,655 mapped
 1,543,248 unMapped (2%)
67,569,903 total

YY1  already mapped to hg18

3. Convert new GFF back to sgr
python ~/bzr-projects/PatternBrowser_gsc_mirror/PatternBrowser-trunk/scripts/customGFFToSgr.py UCD370_CtBP2_H1hES_hg18_customGff/UCD370_CtBP2_H1hES_hg18_liftover.gff UCD370_CtBP2_H1hES_hg18_sgr/UCD370_CtBP2_H1hES_hg18_liftover.sgr 30

Several unexpected window sizes - vast majority close to 30nt, but a few exceptions:

Unexpected window size: 
chr4 3883372 3964524 81152

Unexpected window size: 
chr6 9109233 9272250 163017

Unexpected window size: 
chr8 144822999 144823713 714

4. Convert liftover sgr to wig
python ~/bzr-projects/PatternBrowser_gsc_mirror/PatternBrowser-trunk/scripts/sgrToWig.py UCD370_CtBP2_H1hES_hg18_sgr/UCD370_CtBP2_H1hES_hg18_liftover.sgr UCD370_CtBP2_H1hES_hg18_wig/UCD370_CtBP2_H1hES_hg18_liftover.wig 30 CtBP2 true

CtBP2:
consistent lines:  27521020
inconsistent lines: 2776745 (~10%)

Suz12:
consistent lines:  62854083
inconsistent lines: 3171848 (~5%)

5. Convert original sgr to wig
python ~/bzr-projects/PatternBrowser_gsc_mirror/PatternBrowser-trunk/scripts/sgrToWig.py UCD370_CtBP2_H1hES_hg19_sgr/UCD370_CtBP2_H1hES_hg19_SOLE_rawbinning.sgr UCD370_CtBP2_H1hES_hg19_wig/UCD370_CtBP2_H1hES_hg19_SOLE_rawbinning.wig 30 CtBP2_H1hES_hg19

6. Convert these wigs to bigWigs (too large to load directly)
on xhost06 using header free wigs:
/home/grobertson/bin/x86_64/wigToBigWig -clip UCD370_CtBP2_H1hES_hg18_wig/UCD370_CtBP2_H1hES_hg18_liftover_noHeader.wig /home/grobertson/bin/x86_64/hg18.chrom.sizes UCD370_CtBP2_H1hES_hg18_wig/UCD370_CtBP2_H1hES_hg18_liftover.bw
/home/grobertson/bin/x86_64/wigToBigWig -clip UCD370_CtBP2_H1hES_hg19_wig/UCD370_CtBP2_H1hES_hg19_SOLE_rawbinning_noHeader.wig /home/grobertson/bin/x86_64/hg19.chrom.sizes UCD370_CtBP2_H1hES_hg19_wig/UCD370_CtBP2_H1hES_hg19_SOLE_rawbinning.bw

Upload as: 
track type=bigWig name="CtBP2" description="CtBP2" maxHeightPixels=40:40:20 visibility=full color=50,50,150 priority=1 bigDataUrl=http://www.bcgsc.ca/downloads/cydney-test/testing/test_hg18.bw