e05b985e2e81191b8e46da0afd336382afc66e12 max Fri Aug 29 00:58:40 2025 -0700 adding panmask track, refs #36293 diff --git src/hg/makeDb/doc/hg38/problematic.txt src/hg/makeDb/doc/hg38/problematic.txt index a655cfd802b..55626aefea9 100644 --- src/hg/makeDb/doc/hg38/problematic.txt +++ src/hg/makeDb/doc/hg38/problematic.txt @@ -91,36 +91,40 @@ 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 ############################################################################# + +# Panmask track, Max, Aug 29 2025 +wget https://zenodo.org/records/16755940/files/hg38.pm151b-v3.easy.bed.gz?download=1 +mv hg38.pm151b-v3.easy.bed.gz\?download\=1 hg38.pm151b-v3.easy.bed.gz +bedToBigBed hg38.pm151b-v3.easy.bed.gz ../../../chrom.sizes hg38.pm151b-v3.easy.bb