# for emacs: -*- mode: sh; -*- # This file describes how we made the browser database on # NCBI build 38 (December 2013 freeze) aka: # GRCh38 - Genome Reference Consortium Human Reference 38 # Assembly Accession: GCA_000001405.2 ############################################################################# ## Single Cell Merged - DONE - 2022-04-11 (Jim, Brittney, Jonathan) # Make working directory for a new browser track that merges together many individual # single cell datasets # Existing tracks being incorporated into this merged set: bloodHao, pancreasBaron, # placentaVentoTormo10x, fetalGeneAtlas, kidneySteward, muscleDeMicheli, ileumWang, # cortexVelmeshev, colonWang, heartCellAtlas, liverMacParland, rectumWang, # lungTravaglini2020droplet, skinSoleBoldo mkdir /hive/data/genomes/hg38/bed/singleCell/merged cd /hive/data/genomes/hg38/bed/singleCell/merged # Each dataset can have an independent gene set. So, we need to make up a common gene # set they all can map to. # Reuse some of the code for creating gene sets from collections of mRNA to create # a graph of genes with slight differences in which gene was chosen looking a lot like # splice variants txBedToGraph \ /hive/data/genomes/hg38/bed/singleCell/bloodHao/mapping.bed /hive/data/genomes/hg38/bed/singleCell/bloodHao/mapping.bed \ /hive/data/genomes/hg38/bed/singleCell/pancreasBaron/mapping.bed /hive/data/genomes/hg38/bed/singleCell/pancreasBaron/mapping.bed \ /hive/data/genomes/hg38/bed/singleCell/placentaVentoTormo/10x/mapping.bed /hive/data/genomes/hg38/bed/singleCell/placentaVentoTormo/10x/mapping.bed \ /hive/data/genomes/hg38/bed/singleCell/fetalGeneAtlas/mapping.bed /hive/data/genomes/hg38/bed/singleCell/fetalGeneAtlas/mapping.bed \ /hive/data/genomes/hg38/bed/singleCell/kidneyStewart/mapping.bed /hive/data/genomes/hg38/bed/singleCell/kidneyStewart/mapping.bed \ /hive/data/genomes/hg38/bed/singleCell/muscleDeMicheli/mapping.bed /hive/data/genomes/hg38/bed/singleCell/muscleDeMicheli/mapping.bed \ /hive/data/genomes/hg38/bed/singleCell/ileumWang/mapping.bed /hive/data/genomes/hg38/bed/singleCell/ileumWang/mapping.bed \ /hive/data/genomes/hg38/bed/singleCell/cortexVelmeshev/mapping.bed /hive/data/genomes/hg38/bed/singleCell/cortexVelmeshev/mapping.bed \ /hive/data/genomes/hg38/bed/singleCell/colonWang/mapping.bed /hive/data/genomes/hg38/bed/singleCell/colonWang/mapping.bed \ /hive/data/genomes/hg38/bed/singleCell/heartCellAtlas/mapping.bed /hive/data/genomes/hg38/bed/singleCell/heartCellAtlas/mapping.bed \ /hive/data/genomes/hg38/bed/singleCell/liverMacParland/mapping.bed /hive/data/genomes/hg38/bed/singleCell/liverMacParland/mapping.bed \ /hive/data/genomes/hg38/bed/singleCell/rectumWang/mapping.bed /hive/data/genomes/hg38/bed/singleCell/rectumWang/mapping.bed \ /hive/data/genomes/hg38/bed/singleCell/lungTravaglini2020/droplet/mapping.bed /hive/data/genomes/hg38/bed/singleCell/lungTravaglini2020/droplet/mapping.bed \ /hive/data/genomes/hg38/bed/singleCell/skinSoleBoldo/mapping.bed /hive/data/genomes/hg38/bed/singleCell/skinSoleBoldo/mapping.bed \ all_mapping.txg # Hand wrangle copies of the existing cell_type.stats files for each of those data sets, creating # "cell_type.stats.detailed" files, which include data about organ, stage, cell class, subclass, # cell type, average total, and color (copied from the trackDb entries for the relevant tracks, so that # the merged track colors match those in the individual tracks). # Create a unify.tsv that references those files to then run hcaUnifyMatrix. The weight values will # be ignored when we renormalize. printf "Blood 6 33.5 /hive/data/genomes/hg38/bed/singleCell/bloodHao/mapping.bed /hive/data/genomes/hg38/bed/singleCell/bloodHao/clust/cell_type.matrix /hive/data/genomes/hg38/bed/singleCell/bloodHao/clust/cell_type.refStats /hive/data/genomes/hg38/bed/singleCell/bloodHao/bbi/cell_type.stats.detailed Brain 9 20 /hive/data/genomes/hg38/bed/singleCell/cortexVelmeshev/mapping.bed /hive/data/genomes/hg38/bed/singleCell/cortexVelmeshev/clust/cell_type.matrix /hive/data/genomes/hg38/bed/singleCell/cortexVelmeshev/clust/cell_type.refStats /hive/data/genomes/hg38/bed/singleCell/cortexVelmeshev/bbi/cell_type.stats.detailed Colon 5 40 /hive/data/genomes/hg38/bed/singleCell/colonWang/mapping.bed /hive/data/genomes/hg38/bed/singleCell/colonWang/clust/cell_type.matrix /hive/data/genomes/hg38/bed/singleCell/colonWang/clust/cell_type.refStats /hive/data/genomes/hg38/bed/singleCell/colonWang/bbi/cell_type.stats.detailed Fetal 12 22.5 /hive/data/genomes/hg38/bed/singleCell/fetalGeneAtlas/mapping.bed /hive/data/genomes/hg19/bed/singleCell/fetalGeneAtlas/clust/cell_type.matrix /hive/data/genomes/hg19/bed/singleCell/fetalGeneAtlas/clust/cell_type.refStats /hive/data/genomes/hg38/bed/singleCell/fetalGeneAtlas/bbi/cell_type.stats.detailed Heart 1 40 /hive/data/genomes/hg38/bed/singleCell/heartCellAtlas/mapping.bed /hive/data/genomes/hg38/bed/singleCell/heartCellAtlas/clust/cell_type.matrix /hive/data/genomes/hg38/bed/singleCell/heartCellAtlas/clust/cell_type.refStats /hive/data/genomes/hg38/bed/singleCell/heartCellAtlas/bbi/cell_type.stats.detailed Ileum 5 40 /hive/data/genomes/hg38/bed/singleCell/ileumWang/mapping.bed /hive/data/genomes/hg38/bed/singleCell/ileumWang/clust/cell_type.matrix /hive/data/genomes/hg38/bed/singleCell/ileumWang/clust/cell_type.refStats /hive/data/genomes/hg38/bed/singleCell/ileumWang/bbi/cell_type.stats.detailed Kidney 7 50 /hive/data/genomes/hg38/bed/singleCell/kidneyStewart/mapping.bed /hive/data/genomes/hg38/bed/singleCell/kidneyStewart/clust/cell_type.matrix /hive/data/genomes/hg38/bed/singleCell/kidneyStewart/clust/cell_type.refStats /hive/data/genomes/hg38/bed/singleCell/kidneyStewart/bbi/cell_type.stats.detailed Liver 3 66.5 /hive/data/genomes/hg38/bed/singleCell/liverMacParland/mapping.bed /hive/data/genomes/hg38/bed/singleCell/liverMacParland/clust/cell_type.matrix /hive/data/genomes/hg38/bed/singleCell/liverMacParland/clust/cell_type.refStats /hive/data/genomes/hg38/bed/singleCell/liverMacParland/bbi/cell_type.stats.detailed Lung 10 30 /hive/data/genomes/hg38/bed/singleCell/lungTravaglini2020/droplet/mapping.bed /hive/data/genomes/hg38/bed/singleCell/lungTravaglini2020/droplet/clust/cell_type.matrix /hive/data/genomes/hg38/bed/singleCell/lungTravaglini2020/droplet/clust/cell_type.refStats /hive/data/genomes/hg38/bed/singleCell/lungTravaglini2020/droplet/bbi/cell_type.stats.detailed Muscle 8 50 /hive/data/genomes/hg38/bed/singleCell/muscleDeMicheli/mapping.bed /hive/data/genomes/hg38/bed/singleCell/muscleDeMicheli/clust/cell_type.matrix /hive/data/genomes/hg38/bed/singleCell/muscleDeMicheli/clust/cell_type.refStats /hive/data/genomes/hg38/bed/singleCell/muscleDeMicheli/bbi/cell_type.stats.detailed Pancreas 2 40 /hive/data/genomes/hg38/bed/singleCell/pancreasBaron/mapping.bed /hive/data/genomes/hg38/bed/singleCell/pancreasBaron/clust/cell_type.matrix /hive/data/genomes/hg38/bed/singleCell/pancreasBaron/clust/cell_type.refStats /hive/data/genomes/hg38/bed/singleCell/pancreasBaron/bbi/cell_type.stats.detailed Placenta 4 50 /hive/data/genomes/hg38/bed/singleCell/placentaVentoTormo/10x/mapping.bed /hive/data/genomes/hg38/bed/singleCell/placentaVentoTormo/10x/clust/cell_type.matrix /hive/data/genomes/hg38/bed/singleCell/placentaVentoTormo/10x/clust/cell_type.refStats /hive/data/genomes/hg38/bed/singleCell/placentaVentoTormo/10x/bbi/cell_type.stats.detailed Rectum 5 40 /hive/data/genomes/hg38/bed/singleCell/rectumWang/mapping.bed /hive/data/genomes/hg38/bed/singleCell/rectumWang/clust/cell_type.matrix /hive/data/genomes/hg38/bed/singleCell/rectumWang/clust/cell_type.refStats /hive/data/genomes/hg38/bed/singleCell/rectumWang/bbi/cell_type.stats.detailed Skin 11 80 /hive/data/genomes/hg38/bed/singleCell/skinSoleBoldo/mapping.bed /hive/data/genomes/hg19/bed/singleCell/skinSoleBoldo/clust/cell_type.matrix /hive/data/genomes/hg19/bed/singleCell/skinSoleBoldo/clust/cell_type.refStats /hive/data/genomes/hg38/bed/singleCell/skinSoleBoldo/bbi/cell_type.stats.detailed" > unify.tsv # Create a merged matrix out of individual matrices which are specified in unify.tsv hcaUnifyMatrix all_mapping.txg unify.tsv outMatrix.tsv -bed=out.bed -empty=0 -trackDb=out.ra -stats=singleCellMerged.stats # Convert merged gene matrix and gene sets into a bigBarChart matrixToBarChartBed outMatrix.tsv out.bed barChart.bed bedSort barChart.bed barChart.bed bedToBigBed barChart.bed /hive/data/genomes/hg38/chrom.sizes singleCellMerged.bb -type=bed6+3 -as=/cluster/home/kent/src/hg/lib/simpleBarChartBed.as # Link bigBed and also stats file used by faceted details page to runtime accessible directory ln -s /hive/data/genomes/hg38/bed/singleCell/merged/singleCellMerged.bb /gbdb/hg38/bbi/singleCellMerged/ ln -s /hive/data/genomes/hg38/bed/singleCell/merged/singleCellMerged.stats /gbdb/hg38/bbi/singleCellMerged/ # Add the contents of out.ra to the hg38 trackDb.ra settings along with references to the above files and # some useful barChart track settings. #############################################################################