MISOSetting_splidarEvents.mm9.se.shvar.template

genome=mm9 ###
typeAnno=acembly ###
MISOPATH=/lab/jaenisch_albert/Apps/yarden/MixtureIsoforms/

genomeRootDir=/lab/jaenisch_albert/genomes/

genomeSizes=${genomeRootDir}/${genome}/${genome}_nr.sizes
eventGff=/lab/jaenisch_albert/genomes/mm9/SplidarEventGff/allEvents #####
rawGffFile=/lab/jaenisch_albert/genomes/mm9/SplidarEventGff/allEvents.pe.GFF3 #######

targetBamFileBaseName=accepted_hits.sorted.bam  ### use the sorted one?
readLen=36 ###
pairedEndFlag="" 
clusterFlag="--use-cluster --chunk-jobs 1000"
bamFileSubRoot=tophatOutput
MISOOutSubRoot=MISOOnSE_splidarEvents

misoRunSetting=miso_settings_splidarEvents.txt