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MISOScripts.collapseMISOSplidarEventOnBFAndDiffByEGString.py
MISOScripts.collapseMISOSplidarEventOnBFAndDiffByEGString.py
 
 
MISOSetting.mm9.pe200_20.shvar.template
MISOSetting.mm9.pe200_20.shvar.template
 
 
MISOSetting.mm9.se.shvar.template
MISOSetting.mm9.se.shvar.template
 
 
MISOSetting_acembly.hg18.se.shvar.template
MISOSetting_acembly.hg18.se.shvar.template
 
 
MISOSetting_acembly.mm9.pe.shvar.template
MISOSetting_acembly.mm9.pe.shvar.template
 
 
MISOSetting_acembly.mm9.pe200_20.shvar.template
MISOSetting_acembly.mm9.pe200_20.shvar.template
 
 
MISOSetting_acembly.mm9.se.shvar.template
MISOSetting_acembly.mm9.se.shvar.template
 
 
MISOSetting_burgeSE.mm9.pe.shvar.template
MISOSetting_burgeSE.mm9.pe.shvar.template
 
 
MISOSetting_burgeSE.mm9.pe200_20.shvar.template
MISOSetting_burgeSE.mm9.pe200_20.shvar.template
 
 
MISOSetting_ensGene.mm9.pe200_20.shvar.template
MISOSetting_ensGene.mm9.pe200_20.shvar.template
 
 
MISOSetting_ensGene.mm9.se.shvar.template
MISOSetting_ensGene.mm9.se.shvar.template
 
 
MISOSetting_splidarEvents.hg18.se.shvar.template
MISOSetting_splidarEvents.hg18.se.shvar.template
 
 
MISOSetting_splidarEvents.mm9.pe.shvar.template
MISOSetting_splidarEvents.mm9.pe.shvar.template
 
 
MISOSetting_splidarEvents.mm9.pe200_20.shvar.template
MISOSetting_splidarEvents.mm9.pe200_20.shvar.template
 
 
MISOSetting_splidarEvents.mm9.se.shvar.template
MISOSetting_splidarEvents.mm9.se.shvar.template
 
 
README
README
 
 
cloneTophatOutputByGroup.sh
cloneTophatOutputByGroup.sh
 
 
correctMISOForSplidarEvents.py
correctMISOForSplidarEvents.py
 
 
freeSpace.sh
freeSpace.sh
 
 
freeSpace_fastq.sh
freeSpace_fastq.sh
 
 
makeBamFilesForTophatOutput.sh
makeBamFilesForTophatOutput.sh
 
 
makeExonStringMap.sh
makeExonStringMap.sh
 
 
makeWigFilesForTophatOutput.sh
makeWigFilesForTophatOutput.sh
 
 
miso_settings.txt.template
miso_settings.txt.template
 
 
miso_settings_acembly.txt.template
miso_settings_acembly.txt.template
 
 
miso_settings_burgeEvents.txt
miso_settings_burgeEvents.txt
 
 
miso_settings_burgeEvents.txt.template
miso_settings_burgeEvents.txt.template
 
 
miso_settings_splidarEvents.txt.template
miso_settings_splidarEvents.txt.template
 
 
prepareMISOReducers.sh
prepareMISOReducers.sh
 
 
reduceMISOFileDimensions.py
reduceMISOFileDimensions.py
 
 
retemplate.sh
retemplate.sh
 
 
sashimi_plots_settings.txt
sashimi_plots_settings.txt
 
 
scripturePostProcessing.sh
scripturePostProcessing.sh
 
 
scripturePrepareJobOnTophatFolder.sh
scripturePrepareJobOnTophatFolder.sh
 
 
scriptureRunScripture.sh
scriptureRunScripture.sh
 
 
todoConvertEbedToGff.sh
todoConvertEbedToGff.sh
 
 
todoIndexGff.sh
todoIndexGff.sh
 
 
todoMISOPostStepOne.sh
todoMISOPostStepOne.sh
 
 
todoMISOSashimiPlots.sh
todoMISOSashimiPlots.sh
 
 
todoMISOStepFiveSplidarDivideEvents.sh
todoMISOStepFiveSplidarDivideEvents.sh
 
 
todoMISOStepFourRemapToIsoformNames.sh
todoMISOStepFourRemapToIsoformNames.sh
 
 
todoMISOStepFourRemapToIsoformNames.sh.bak
todoMISOStepFourRemapToIsoformNames.sh.bak
 
 
todoMISOStepOneEventAnalysis.sh
todoMISOStepOneEventAnalysis.sh
 
 
todoMISOStepOnePrimeReduceMISOFileDimension.sh
todoMISOStepOnePrimeReduceMISOFileDimension.sh
 
 
todoMISOStepPostZeroInsertLengthDistSummarize.sh
todoMISOStepPostZeroInsertLengthDistSummarize.sh
 
 
todoMISOStepThreeDetectDifferential.sh
todoMISOStepThreeDetectDifferential.sh
 
 
todoMISOStepThreeDetectDifferentialSpecifyingComparisons.sh
todoMISOStepThreeDetectDifferentialSpecifyingComparisons.sh
 
 
todoMISOStepTwoSummarize.sh
todoMISOStepTwoSummarize.sh
 
 
todoMISOStepZeroInsertLengthDist.sh
todoMISOStepZeroInsertLengthDist.sh
 
 
todoRPKM.sh
todoRPKM.sh
 
 
todoRPKMPostProc.sh
todoRPKMPostProc.sh
 
 
untemplate.sh
untemplate.sh
 
 

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untemplate the shvar files by

bash untemplate.sh

then, modify the setting files.

use the appropriate setting files.

*** IMPORTANT ***

modify in the shvar file the readLen variable.

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For running and controlling miso

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