3a91631b10c28b2f0f4d0f51ce2db8cbd9dee0a7
braney
  Sat Aug 12 16:13:11 2023 -0700
instructions for hprc arrangement tracks

diff --git src/hg/makeDb/doc/hg38/hprcRearrange.txt src/hg/makeDb/doc/hg38/hprcRearrange.txt
new file mode 100644
index 0000000..93ad8c0
--- /dev/null
+++ src/hg/makeDb/doc/hg38/hprcRearrange.txt
@@ -0,0 +1,57 @@
+# 2023-08-12 braney
+
+VERSION=V1
+inversion=hprcArrInv$VERSION
+duplication=hprcArrDup$VERSION
+all=hprcArrAll$VERSION
+
+mkdir -p /cluster/data/hg38/bed/hprcArrange$VERSION
+cd /cluster/data/hg38/bed/hprcArrange$VERSION
+
+# grab the chains
+ls /hive/data/genomes/hg38/bed/hprc/bigChains/*.bb | grep -v Link > bigChain.lst
+ls /hive/data/genomes/hg38/bed/hprc/bigChains/*.bb | grep Link > bigLink.lst
+paste bigChain.lst bigLink.lst > both.lst
+
+rm -rf inversions duplications
+mkdir inversions duplications
+
+# make the job that will figure out the inversions and duplications in each assembly
+while read chain link 
+do
+name=`basename $chain | sed 's?-.*??' | sed 's/.bb//'`
+echo bigChainArrange $chain $link $name inversions/$name.txt duplications/$name.txt
+done < both.lst > jobs
+
+para make jobs
+
+# create the inversion bigBed and bigWig
+cat inversions/* |sort -k1,1 -k2,2n | bedCollect stdin $inversion.bed
+bedToBigBed  $inversion.bed /cluster/data/hg38/chrom.sizes $inversion.bb -as=$HOME/kent/src/hg/lib/chainArrange.as -type=bed9+1
+cat inversions/* | sort -k1,1 | bedItemOverlapCount hg38 stdin > $inversion.bedGraph
+bedGraphToBigWig $inversion.bedGraph /cluster/data/hg38/chrom.sizes $inversion.bw
+mkdir -p /gbdb/hg38/hprcArr$VERSION
+rm -f  /gbdb/hg38/hprcArr$VERSION/$inversion.*
+ln -s `pwd`/$inversion.bw /gbdb/hg38/hprcArr$VERSION
+ln -s `pwd`/$inversion.bb /gbdb/hg38/hprcArr$VERSION
+
+# create the duplications bigBed and bigWig
+cat duplications/* |sort -k1,1 -k2,2n | bedCollect stdin $duplication.bed
+bedToBigBed  $duplication.bed /cluster/data/hg38/chrom.sizes $duplication.bb -as=$HOME/kent/src/hg/lib/chainArrange.as -type=bed9+1
+cat duplications/* | sort -k1,1 | bedItemOverlapCount hg38 stdin > $duplication.bedGraph
+bedGraphToBigWig $duplication.bedGraph /cluster/data/hg38/chrom.sizes $duplication.bw
+mkdir -p /gbdb/hg38/hprcArr$VERSION
+rm -f  /gbdb/hg38/hprcArr$VERSION/$duplication.*
+ln -s `pwd`/$duplication.bw /gbdb/hg38/hprcArr$VERSION
+ln -s `pwd`/$duplication.bb /gbdb/hg38/hprcArr$VERSION
+
+# create the sum of duplications and inversions bigBed and bigWig
+cat inversions/* duplications/* |sort -k1,1 -k2,2n | bedCollect stdin $all.bed
+bedToBigBed  $all.bed /cluster/data/hg38/chrom.sizes $all.bb -as=$HOME/kent/src/hg/lib/chainArrange.as -type=bed9+1
+cat inversions/* duplications/* | sort -k1,1 | bedItemOverlapCount hg38 stdin > $all.bedGraph
+bedGraphToBigWig $all.bedGraph /cluster/data/hg38/chrom.sizes $all.bw
+mkdir -p /gbdb/hg38/hprcArr$VERSION
+rm -f  /gbdb/hg38/hprcArr$VERSION/$all.*
+ln -s `pwd`/$all.bw /gbdb/hg38/hprcArr$VERSION
+ln -s `pwd`/$all.bb /gbdb/hg38/hprcArr$VERSION
+