687239fe5e1d9407369eb985448dc1f844b261b0 gperez2 Tue Nov 5 11:24:23 2024 -0800 Moving the programaticGIAB.txt text to the problematic.txt makedoc, refs #32715 diff --git src/hg/makeDb/doc/hg38/problematicGIAB.txt src/hg/makeDb/doc/hg38/problematicGIAB.txt deleted file mode 100644 index 2496204..0000000 --- src/hg/makeDb/doc/hg38/problematicGIAB.txt +++ /dev/null @@ -1,49 +0,0 @@ -############################################################################# -# problematicGIAB: Difficult regions from GIAB via NCBI - Megna/Gerardo -# Redmine #34253 - -# Megna workflow for v3.3: -cp /cluster/home/mchalama/public_html/tracks/CoLoRSdb/genomes.txt /cluster/home/mchalama/public_html/tracks/difficult -cp /cluster/home/mchalama/public_html/tracks/CoLoRSdb/hub.txt /cluster/home/mchalama/public_html/tracks/difficult -cp /cluster/home/mchalama/public_html/tracks/CoLoRSdb/hg38/CoLoRSdb.html /cluster/home/mchalama/public_html/tracks/difficult -cp /cluster/home/mchalama/public_html/tracks/CoLoRSdb/hg38/trackDb.txt /cluster/home/mchalama/public_html/tracks/difficult -mkdir hg38 -mv /cluster/home/mchalama/public_html/tracks/difficult/CoLoRSdb.html /cluster/home/mchalama/public_html/tracks/difficult/hg38 -mv /cluster/home/mchalama/public_html/tracks/difficult/trackDb.txt /cluster/home/mchalama/public_html/tracks/difficult/hg38 -edit genomes.txt -edit hub.txt; got contact of PI from here: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.3/README.md -wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.3/GRCh38@all/Union/GRCh38_alldifficultregions.bed.gz -wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.3/GRCh38@all/Union/GRCh38_alllowmapandsegdupregions.bed.gz -wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.3/GRCh38@all/Union/GRCh38_notinalldifficultregions.bed.gz -wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.3/GRCh38@all/Union/GRCh38_notinalllowmapandsegdupregions.bed.gz -#edit trackDb.txt to include the 4 datasets -#Bed to BigBed conversion because I realized you can't see beds properly on the hub -bedToBigBed /cluster/home/mchalama/public_html/tracks/difficult/hg38/GRCh38_alldifficultregions.bed.gz /cluster/home/mchalama/public_html/tracks/difficult/hg38.chrom.sizes GRCh38_alldifficultregions.bb -bedToBigBed /cluster/home/mchalama/public_html/tracks/difficult/hg38/GRCh38_alllowmapandsegdupregions.bed.gz /cluster/home/mchalama/public_html/tracks/difficult/hg38.chrom.sizes GRCh38_alllowmapandsegdupregions.bb -bedToBigBed /cluster/home/mchalama/public_html/tracks/difficult/hg38/GRCh38_notinalldifficultregions.bed.gz /cluster/home/mchalama/public_html/tracks/difficult/hg38.chrom.sizes GRCh38_notinalldifficultregions.bb -bedToBigBed /cluster/home/mchalama/public_html/tracks/difficult/hg38/GRCh38_notinalllowmapandsegdupregions.bed.gz /cluster/home/mchalama/public_html/tracks/difficult/hg38.chrom.sizes GRCh38_notinalllowmapandsegdupregions.bb -edit the html file to include information about the track -#open genome browser -#navigate to custom hub and paste the following URL -#https://hgwdev.gi.ucsc.edu/~mchalama/tracks/difficult/hub.txt - - -# Gerardo workflow for v3.5: -# Copied the trackDb.txt into the human/hg38/problematic.ra and copied html description into problematic html -# Downloaded the v3.5 data -cd /hive/data/genomes/hg38/bed/ -mkdir problematic; cd problematic -mkdir GIAB; cd GIAB -wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/GRCh38@all/Union/GRCh38_alldifficultregions.bb -wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/GRCh38@all/Union/GRCh38_alllowmapandsegdupregions.bb -wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/GRCh38@all/Union/GRCh38_notinalldifficultregions.bb -wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/GRCh38@all/Union/GRCh38_notinalllowmapandsegdupregions.bb -cd /gbdb/hg38/ -mkdir problematic; cd problematic -mkdir GIAB; cd GIAB -# Made symlinks -ln -s /hive/data/genomes/hg38/bed/problematic/GIAB/alldifficultregions.bb -ln -s /hive/data/genomes/hg38/bed/problematic/GIAB/notinalldifficultregions.bb -ln -s /hive/data/genomes/hg38/bed/problematic/GIAB/alllowmapandsegdupregions.bb -ln -s /hive/data/genomes/hg38/bed/problematic/GIAB/notinalllowmapandsegdupregions.bb -# Updated the bigDataUrl problematic.ra and problematic.html