MISOSetting_acembly.mm9.pe.shvar.template

genome=mm9 ###
typeAnno=acembly ###


genomeRootDir=/lab/jaenisch_albert/genomes/

genomeSizes=${genomeRootDir}/${genome}/${genome}_nr.sizes
eventGff=${genomeRootDir}/${genome}/annos/${typeAnno} ###
rawGffFile=${genomeRootDir}/${genome}/annos/${typeAnno}.pe.gff3 ##
rawEbedFile=${genomeRootDir}/${genome}/annos/${typeAnno}.ebed  ###

targetBamFileBaseName=accepted_hits.sorted.bam  ### use the sorted one?
readLen= ###

  
clusterFlag="--use-cluster --chunk-jobs 600"
bamFileSubRoot=tophatOutput
MISOOutSubRoot=MISOOnPE_acembly

misoRunSetting=miso_settings_acembly.txt

bfThresholds[0]=5
bfThresholds[1]=20
bfThresholds[2]=100


constExonGff=/lab/solexa_jaenisch/jaenisch_albert/genomes/mm9/burgeLabEvents/const_exons/exons.chrSN/Mus_musculus.NCBIM37.65.chrSN.min_1000.const_exons.gff
useInsertLenStat=yes


dPsiCutOffs[0]=0.1
dPsiCutOffs[1]=0.2
dPsiCutOffs[2]=0.3
dPsiCutOffs[3]=0.5