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# problematicGIAB: Difficult regions from GIAB via NCBI - Megna/Gerardo
# Redmine #34253

# Megna workflow:
cd /cluster/home/mchalama/public_html/tracks/
mkdir T2Tdiff
cd T2Tdiff
mkdir hs1
cd hs1
cp -r /cluster/home/mchalama/public_html/tracks/difficult /cluster/home/mchalama/public_html/tracks/T2Tdiff
mv /cluster/home/mchalama/public_html/tracks/difficult/genomes.txt /cluster/home/mchalama/public_html/tracks/T2Tdiff
mv /cluster/home/mchalama/public_html/tracks/difficult/hub.txt /cluster/home/mchalama/public_html/tracks/T2Tdiff
mv /cluster/home/mchalama/public_html/tracks/difficult/drfGvN.html  /cluster/home/mchalama/public_html/tracks/T2Tdiff/hs1
mv /cluster/home/mchalama/public_html/tracks/difficult/trackDb.txt /cluster/home/mchalama/public_html/tracks/T2Tdiff/hs1
nano /cluster/home/mchalama/public_html/tracks/T2Tdiff/genomes.txt
nano /cluster/home/mchalama/public_html/tracks/T2Tdiff/hub.txt
nano /cluster/home/mchalama/public_html/tracks/T2Tdiff/hs1/trackDb.txt
cd /cluster/home/mchalama/public_html/tracks/T2Tdiff/hs1
wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/CHM13@all/Union/CHM13_alldifficultregions.bb
wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/CHM13@all/Union/CHM13_alllowmapandsegdupregions.bb
wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/CHM13@all/Union/CHM13_notinalldifficultregions.bb
wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/CHM13@all/Union/CHM13_notinalllowmapandsegdupregions.bb
open genome browser

# Gerardo workflow
cd /hive/data/genomes/hs1/bed/
mkdir problematic; cd problematic
mkdir GIAB; cd GIAB
wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/CHM13@all/Union/CHM13_alldifficultregions.bb 
wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/CHM13@all/Union/CHM13_alllowmapandsegdupregions.bb
wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/CHM13@all/Union/CHM13_notinalldifficultregions.bb
wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/CHM13@all/Union/CHM13_notinalllowmapandsegdupregions.bb
mv CHM13_notinalllowmapandsegdupregions.bb notinalllowmapandsegdupregions.bb
mv CHM13_alllowmapandsegdupregions.bb alllowmapandsegdupregions.bb
mv CHM13_alldifficultregions.bb alldifficultregions.bb
mv CHM13_notinalldifficultregions.bb notinalldifficultregions.bb
cd /gbdb/hs1/
mkdir problematic; cd problematic
mkdir GIAB; cd GIAB
# Made symlinks
ln -s /hive/data/genomes/hs1/bed/problematic/GIAB/notinalllowmapandsegdupregions.bb
ln -s /hive/data/genomes/hs1/bed/problematic/GIAB/alllowmapandsegdupregions.bb
ln -s /hive/data/genomes/hs1/bed/problematic/GIAB/alldifficultregions.bb
ln -s /hive/data/genomes/hs1/bed/problematic/GIAB/notinalldifficultregions.bb
cd /cluster/home/gperez2/kent/src/hg/makeDb/trackDb/human/hs1
cp /cluster/home/mchalama/public_html/tracks/T2Tdiff/hs1/trackDb.txt problematic.ra
cp /cluster/home/mchalama/public_html/tracks/T2Tdiff/hs1/drfGvN.html problematic.html
# Updated the problematic.ra, problematic.html, and human/hs1/trackDb.ra
