ec3d64b274d7d36030ea54d86ecdb96afc18f35d
kent
  Wed Aug 25 10:56:56 2021 -0700
Updating path to cell browser matrix and meta.tsv.

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index ddce385..6a3e2f6 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -34335,47 +34335,47 @@
     ln -s /hive/data/genomes/hg19/bed/singleCell/skinSoleBoldo/bbi/$s.stats /gbdb/hg19/bbi/skinSoleBoldo/
 end
 
 # Add the bits from clust/*.ra and clust/*.colors to hg19/trackDb.ra and you should be good.
 rm -f tracks.ra
 foreach s (cell_type donor age age_cell_type)
     grep -v barChartColors clust/$s.ra >>tracks.ra
     cat clust/$s.colors >> tracks.ra
     echo transformFunc NONE >> tracks.ra
     echo barChartLimit 2 >> tracks.ra
     echo "" >> tracks.ra
 end
 
 
 #############################################################################
-# fetalGeneAtlas JimK 01-19-2020
+# fetalGeneAtlas JimK 01-19-2021
 ############################################################################
 # This is the RNA-seq part of the data set described in
 # "A human cell atlas of fetal gene expression" by Cao, Day et al
 # Science 13 Nove 2020.   This was imported from Cell Browser
 
 # Create directory for work.
 
 mkdir -p /hive/data/genomes/hg19/bed/singleCell/fetalGeneAtlas
 cd /hive/data/genomes/hg19/bed/singleCell/fetalGeneAtlas
 
 # Create output dir for binaries
 mkdir bbi
 
 # link in in files from cell browser
-ln -s /hive/data/inside/cells/datasets/fetal-gene-atlas/genes/all/meta.tsv .
-ln -s /hive/data/inside/cells/datasets/fetal-gene-atlas/genes/all/exprMatrix.tsv.gz .
+ln -s /hive/data/inside/cells/datasets/fetal-gene-atlas/all/meta.tsv .
+ln -s /hive/data/inside/cells/datasets/fetal-gene-atlas/all/exprMatrix.tsv.gz .
 
 # Get the first line (fields) out of meta.tsv and also make stats on it
 head -1 meta.tsv > meta.fields
 tabInfo meta.tsv -vals=20 > meta.20
 
 
 # Make a bunch of smaller matrices by clustering columns.  Mostly we'll use the cluster one
 # but some of the others are good to look at sometimes too.  This is the time consuming step.
 mkdir clust
 matrixClusterColumns -makeIndex=clust/exprMatrix.ix  exprMatrix.tsv.gz meta.tsv \
     Main_cluster_name clust/cell_type.matrix bbi/cell_type.stats \
     Assay clust/Assay.matrix bbi/Assay.stats \
     Experiment_batch clust/Experiment_batch.matrix bbi/Experiment_batch.stats \
     Fetus_id clust/donor.matrix bbi/donor.stats \
     Organ clust/Organ.matrix bbi/Organ.stats \