e7bfc71ae21d7da0b0b5001c651d5ba1586e99c6 lrnassar Wed Jun 29 18:44:29 2022 -0700 Creating metaDome track, refs #23883 diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt index 2505ade..43e2b7e 100644 --- src/hg/makeDb/doc/hg19.txt +++ src/hg/makeDb/doc/hg19.txt @@ -34881,15 +34881,38 @@ # Sorting the bed files sort -k1,1 -k2,2n Illumina_450k.bed > illumina_450k.bed.sorted sort -k1,1 -k2,2n Illumina_EPIC.bed > illumina_EPIC.bed.sorted # creating a bigBed from the bed files wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes bedToBigBed -type=bed4 illumina_450k.bed.sorted hg19.chrom.sizes illumina_450k.hg19.bb bedToBigBed -type=bed4 illumina_EPIC.bed.sorted hg19.chrom.sizes illumina_EPIC.hg19.bb # Moving data into /hive and creating symlinks in /gbdb cp illumina_450k.hg19.bb /hive/data/genomes/hg19/bed/illumina/illumina_450K.bb cp illumina_EPIC.hg19.bb /hive/data/genomes/hg19/bed/illumina/illumina_EPIC_850K.bb ln -s /hive/data/genomes/hg19/bed/illumina/illumina_450K.bb /gbdb/hg19/bbi/illumina/ilumina450K.bb ln -s /hive/data/genomes/hg19/bed/illumina/illumina_EPIC_850K.bb /gbdb/hg19/bbi/illumina/epic850K.bb + +############################################################################# +# MetaDome refs #23883 (2022-06-29 Lou) + +mkdir /hive/data/genomes/hg19/bed/metaDome/ +cd /hive/data/genomes/hg19/bed/metaDome/ +#scp the data to the dir provided by author via email + +#create .as file for bigBed +#table metaDome +#"MetaDome constraint metrics" +#( +#string chrom; "Reference sequence chromosome or scaffold" +#uint chromStart; "Start position of feature on chromosome" +#uint chromEnd; "End position of feature on chromosome" +#string name; "Combination of chrom+chromStart" +#float score; "MetaDome tolerance score" +#char[1] strand; "+ or - for strand" +#float spID; "Coverage score of homologous positions" +#) + +fetchChromSizes hg19 > hg19.chrom.sizes +python3 ~/kent/src/hg/makeDb/scripts/metaDome/buildMetaDomeTracks.py