bff7103f9b04262250a790222c23f05ed298ed10
max
  Mon Mar 7 03:08:56 2022 -0800
adding docs page and colors for agilent track, refs #23591

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index d831a2b..d4b98e0 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -13795,30 +13795,37 @@
 ln -s 014950_D_BED_20100501.bed agilentCgh4x44k.bed
 ln -s 021924_D_BED_20100501.bed agilentCgh8x60k.bed
 ln -s 028081_D_BED_20101014.bed agilentCghSnp2x400k.bed
 ln -s 029830_D_BED_20100922.bed agilentCghSnp4x180k.bed
 ln -s 023642_D_BED_20100430.bed agilentHrd1x1m.bed
 for bed in agilent*.bed; do
     tail -n +2 $bed | hgLoadBed hg19 ${bed%.bed} stdin
 done
 rm bed.tab
 ### Update (2011-11-01 Andy Pohl
 # (acquired bed file in e-mail attachment)
 cd /hive/data/genomes/hg19/bed/agilentProbes
 ln -s 030587_D_BED_20101006_Colored.bed agilentCghSnpCancer4x180k.bed
 tail +3 agilentCghSnpCancer4x180k.bed | hgLoadBed hg19 agilentCghSnpCancer4x180k stdin
 
+### Update (2022-03-07 Max Haeussler and Daniel Schmelter)
+cd /hive/data/genomes/hg19/bed/agilentProbes/genetiSureCyto
+for i in hg19*.bed; do egrep -v 'browser|track' $i > /tmp/temp.bed; bedSort /tmp/temp.bed /tmp/temp.bed; bedToBigBed /tmp/temp.bed ../../../chrom.sizes `basename $i .bed`.bb; done
+mkdir /gbdb/hg19/genotypeArrays
+cd /gbdb/hg19/genotypeArrays
+for $i in /hive/data/genomes/hg19/bed/agilentProbes/genetiSureCyto/*.bb; do ln -s $i; done
+
 
 #################################################################################
 # Rfam (2011-11-30 Melissa Cline)
 #
 # This contains genomic alignments of Rfam sequences, from the Rfam group.
 #
 # This data is used in building UCSC Genes.
 #
 cd /hive/data/outside/Rfam
 mkdir 111130
 cd 111130
 wget ftp://ftp.sanger.ac.uk/pub/databases/Rfam/CURRENT/genome.gff3.tar.gz
 tar xzvf genome.gff3.tar.gz
 mkdir hg19
 cat /hive/data/genomes/hg19/chrom.aliases \
@@ -34080,30 +34087,34 @@
 
 
 # MGI Datasets:
 
 Track: MGI - Easy Exome Capture V4 Target Regions
 Download: https://en.mgitech.cn/Uploads/Temp/file/20191225/5e03126e808a0.zip
 File name: MGI_Exome_Capture_V4.bed
 
 Track: MGI - Easy Exome Capture V5 Target Regions
 Download: https://en.mgitech.cn/Uploads/Temp/file/20191225/5e0312a7be43e.zip
 File name: MGI_Exome_Capture_V5.bed
 
 # Agilent Datasets:
 Download for all Agilent files: https://earray.chem.agilent.com/suredesign/ - Password needed (from Ana)
 
+to get them:
+go to https://earray.chem.agilent.com/suredesign/ then select Find Designs -> CGH -> Agilent Catalog
+(HT to Daniel)
+
 Track: Agilent - SureSelect Clinical Research Exome Covered by Probes
 File name: S06588914_Covered.bed
 
 Track: Agilent - SureSelect Clinical Research Exome Target Regions
 File name: S06588914_Regions.bed
 
 Track: Agilent - SureSelect Clinical Research Exome V2 Covered by Probes
 File name: S30409818_Covered.bed
 
 Track: Agilent - SureSelect Clinical Research Exome V2 Target Regions
 File name: S30409818_Regions.bed
 
 Track: Agilent - SureSelect Focused Exome Covered by Probes
 File name: S07084713_Covered.bed