aa80d65a1312c44a1c41488390f324f76beb8984
Merge parents c04d210 3a4325f
max
  Tue Apr 5 04:35:24 2022 -0700
Adding Jarvis makedoc. Merge branch 'master' of hgwdev.gi.ucsc.edu:/data/git/kent

Conflicts:
src/hg/makeDb/doc/hg19.txt

diff --cc src/hg/makeDb/doc/hg19.txt
index c55544d,2066151..9fd19c6
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@@ -34749,25 -34749,68 +34749,75 @@@
  cd panelApp
  ln -s /hive/data/genomes/hg19/bed/panelApp/genesPanel.bb
  ln -s /hive/data/genomes/hg19/bed/panelApp/STRsPanel.bb
  cd ~/kent/src/hg/makeDb/trackDb/human/hg19
  wget https://hgwdev.gi.ucsc.edu/~bnguy/panel/hg19/panelapp.html
  cd ~/kent/src/hg/makeDb/trackDb
  mv human/hg19/panelapp.html human/hg19/panelApp.html
  curl https://hgwdev.gi.ucsc.edu/~bnguy/panel/hg19/trackDb.txt >> trackDb.ra
  vi trackDb.ra
  make alpha DBS=hg19
  
  ###############################################
  
  #Probe and Microarray data sets addition 3/11/21
  
 +###############################################
 +# Jarvis, Max, 03/28/22
 +cd /hive/data/genomes/hg19/bed/jarvis
 +# downloaded from https://az.app.box.com/v/jarvis-gwrvis-scores/folder/146728772904 by Luis into orig/
 +cd orig
 +zcat `ls | sort | grep bed` > ../jarvis.bed
 +bedGraphToBigWig jarvis.bed ../chrom.sizes jarvis.bw
 +# Go to Brian's cube, push "that was easy" button
 +
+ #############################################################################
+ # chm13 liftover alignments  (2022-03-29 markd)
+ 
+ # preliminary CHM13 <-> hg19 liftOver chains until NCBI produces consensus alignments
+ # provide by Nae-Chyun Chen <naechyun.chen@gmail.com>
+ 
+     mkdir -p /hive/data/genomes/hg19/bed/chm13LiftOver
+     cd /hive/data/genomes/hg19/bed/chm13LiftOver
+ 
+ # Obtain GRCh37 from T2T Globus: team-liftover/v1_nflo/grch37-chm13v2.chain
+ 
+ # rename to better match UCSC convetions and compress
+     mv grch37-chm13v2.chain hg19-chm13v2.over.chain
+     pigz hg19-chm13v2.over.chain
+ 
+ # make NCBI query names as well, since chromAlias doesn't work yet for click-through
+ # note doc is wrong in chromToPsl PSL query is 10
+     chainToPslBasic hg19-chm13v2.over.chain.gz stdout | chromToUcsc -k 10 -a /hive/data/genomes/asmHubs/genbankBuild/GCA/009/914/755/GCA_009914755.4_CHM13_T2T_v2.0/GCA_009914755.4_CHM13_T2T_v2.0.chromAlias.txt | pslToChain stdin stdout | pigz -c > hg19-chm13v2.ncbi-qnames.over.chain.gz
+ 
+ # build bigChain files:
+     hgLoadChain -noBin -test none bigChain hg19-chm13v2.over.chain.gz 
+     sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}' > bigChainIn.tab
+     bedToBigBed -type=bed6+6 -as=${HOME}/kent/src/hg/lib/bigChain.as -tab bigChainIn.tab ../../chrom.sizes hg19-chm13v2.over.chain.bb
+     tawk '{print $1, $2, $3, $5, $4}' link.tab | csort -k1,1 -k2,2n --parallel=64 > bigLinkIn.tab
+     bedToBigBed -type=bed4+1 -as=${HOME}/kent/src/hg/lib/bigLink.as -tab bigLinkIn.tab  ../../chrom.sizes hg19-chm13v2.over.link.bb
+ 
+ # build bigChain with NCBI names files:
+     hgLoadChain -noBin -test none bigChain hg19-chm13v2.ncbi-qnames.over.chain.gz 
+     sed 's/\.000000//' chain.tab | awk 'BEGIN {OFS="\t"} {print $2, $4, $5, $11, 1000, $8, $3, $6, $7, $9, $10, $1}' > bigChainIn.tab
+     bedToBigBed -type=bed6+6 -as=${HOME}/kent/src/hg/lib/bigChain.as -tab bigChainIn.tab ../../chrom.sizes hg19-chm13v2.ncbi-qnames.over.chain.bb
+     tawk '{print $1, $2, $3, $5, $4}' link.tab | csort -k1,1 -k2,2n --parallel=64 > bigLinkIn.tab
+     bedToBigBed -type=bed4+1 -as=${HOME}/kent/src/hg/lib/bigLink.as -tab bigLinkIn.tab  ../../chrom.sizes hg19-chm13v2.ncbi-qnames.over.link.bb
+ 
+     rm *.tab
+    
+ # link to gbdb
+   mkdir -p /gbdb/hg19/bbi/chm13LiftOver
+   ln -sf $(pwd)/*.bb /gbdb/hg19/bbi/chm13LiftOver/
+ 
+ # make downloads, can't add to liftOver directory due to license in that directory
+   mkdir -p /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/chm13LiftOver/
+   ln -sf $(pwd)/hg19-chm13v2.*.chain.gz /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/chm13LiftOver/
+   
+ # push these files
+   /gbdb/hg19/bbi/chm13LiftOver/hg19-chm13v2.ncbi-qnames.over.chain.bb
+   /gbdb/hg19/bbi/chm13LiftOver/hg19-chm13v2.ncbi-qnames.over.link.bb
+   /gbdb/hg19/bbi/chm13LiftOver/hg19-chm13v2.over.chain.bb
+   /gbdb/hg19/bbi/chm13LiftOver/hg19-chm13v2.over.link.bb
+   /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/chm13LiftOver/hg19-chm13v2.ncbi-qnames.over.chain.gz
+   /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/chm13LiftOver/hg19-chm13v2.over.chain.gz
  
 -  
 -#############################################################################