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2020-03-18 markd Rhesus synteny track 25kb, 1mb, and 25mb resolutions

  cd analysis/synteny/tmp

  # do alignments with Rhesus as query
  fgrep -v Rhesus ../../../data/leaf-genomes.lst >targets.lst
  ../../../bin/halStats --bedSequences Rhesus ../../../data/primates_eichler.hal > Rhesus-seqs.bed
  cut -f 1 Rhesus-seqs.bed >Rhesus.seqs

  desired command is:
    ../../../bin/halSynteny --minBlockSize 25000 --maxAnchorDistance 25000 --targetGenome ${TARGET} --queryGenome Rhesus --queryChromosome ${CHROM}  ../../../data/primates_eichler.hal out/${TARGET}.${CHROM}.psl
  which is executed by runSynteny
  
  create syn.tmpl:
    #LOOP
    ../../../primates-2020/bin/runSynteny Rhesus $(path2) $(path1) {check out exists out/$(path1).$(path2).psl}
    #ENDLOOP
  gensub2 targets.lst Rhesus.seqs syn.tmpl syn.jobs
  # run with -ram=16g
  para create -batch=b1 syn.jobs -ram=16g  -maxQueue=100000000

  # build bigPsls
  for o in $(cat targets.lst) ; do (cat out/$o.*.psl | pslSwap stdin stdout >$o-Rhesus.syn25kb.psl &) ; done
  for f in *.psl ; do (pslToBigPsl $f stdout  | sort -k1,1 -k2,2n >$(basename $f .psl).bigPslInput&) ; done  
  for f in *.bigPslInput ; do (bedToBigBed -type=bed12+13 -tab -as=${HOME}/kent/src/hg/lib/bigPsl.as $f ../../../data/Rhesus.chrom.sizes $(basename $f .bigPslInput).bigPsl&) ; done
 
 ### for 1mb resolution
 as above with:
    ../../../primates-2020/bin/runSynteny1mb Rhesus $(path2) $(path1) {check out exists out/$(path1).$(path2).psl}

  # need to increase stack since in bedToBigBed do to very large PSLs
  for o in $(cat targets.lst) ; do (cat out/$o.*.psl | pslSwap stdin stdout >$o-Rhesus.syn1mb.psl &) ; done
  for f in *.psl ; do (pslToBigPsl $f stdout  | sort -k1,1 -k2,2n >$(basename $f .psl).bigPslInput&) ; done  
  for f in *.bigPslInput ; do (ulimit -s 20000; bedToBigBed -type=bed12+13 -tab -as=${HOME}/kent/src/hg/lib/bigPsl.as $f ../../../data/Rhesus.chrom.sizes $(basename $f .bigPslInput).bigPsl&) ; done

### for 25mb resolution, 1mb anchor
 as above with:
    ../../../primates-2020/bin/runSynteny25mb Rhesus $(path2) $(path1) {check out exists out/$(path1).$(path2).psl}

 use 1mb max anchor distance
  # need to increase stack since in bedToBigBed do to very large PSLs
  for o in $(cat targets.lst) ; do (cat out/$o.*.psl | pslSwap stdin stdout >$o-Rhesus.syn25mb.psl &) ; done
  for f in *.psl ; do (pslToBigPsl $f stdout  | sort -k1,1 -k2,2n >$(basename $f .psl).bigPslInput&) ; done  
  for f in *.bigPslInput ; do (ulimit -s 20000; bedToBigBed -type=bed12+13 -tab -as=${HOME}/kent/src/hg/lib/bigPsl.as $f ../../../data/Rhesus.chrom.sizes $(basename $f .bigPslInput).bigPsl&) ; done
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# 2020-04-19 markd browser directory of filter novel exon set

~markd/public_html/primates-2020/rhemac2-novel

bedToHtmlDir -browser-url http://genome.ucsc.edu -title 'High-confidence unique Rhesus exons' -hub http://courtyard.gi.ucsc.edu/~jcarmstr/cat_data/primates_evan/out/trackHub/hub.txt rheMac10 notebooks/rhesus_filtered_novel_exons.bed ~/public_html/primates-2020/rhemac2-novel

http://courtyard.gi.ucsc.edu/~markd/primates-2020/rhemac2-novel/
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