GitHub - albertwcheng/miso-scripts: For running and controlling miso

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Name		Name	Last commit message	Last commit date
Latest commit History 84 Commits
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

Repository files navigation

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.