woldlab.caltech.edu Git - erange.git/commit

author	Sean Upchurch <sau@caltech.edu>
	Wed, 19 Jun 2013 18:56:48 +0000 (11:56 -0700)
committer	Sean Upchurch <sau@caltech.edu>
	Wed, 19 Jun 2013 18:56:48 +0000 (11:56 -0700)
commit	4ad5495359e4322da39868020a7398676261679e
tree	dd80f0b279663f62db95785cad74f5529ca523d9	tree \| snapshot
parent	cfc5602b26323ad2365295145e3f6c622d912eb4	commit \| diff

convert standard analysis pipelines to use bam format natively

27 files changed:

ReadDataset.py		diff \| blob \| history
Region.py		diff \| blob \| history
bamPreprocessing.py	[new file with mode: 0644]	blob
checkrmask.py		diff \| blob \| history
combineRPKMs.py		diff \| blob \| history
combinerds.py		diff \| blob \| history
commoncode.py		diff \| blob \| history
docs/README.chip-seq		diff \| blob \| history
docs/RNA-seq.analysisSteps.txt		diff \| blob \| history
docs/runRNAPairedAnalysis.sh		diff \| blob \| history
docs/runSNPAnalysis.sh		diff \| blob \| history
docs/runStandardAnalysis.sh		diff \| blob \| history
docs/runStrandedAnalysis.sh		diff \| blob \| history
findall.py		diff \| blob \| history
geneLocusBins.py		diff \| blob \| history
geneMrnaCounts.py		diff \| blob \| history
geneMrnaCountsWeighted.py		diff \| blob \| history
geneStartBins.py		diff \| blob \| history
getsplicefa.py		diff \| blob \| history
normalizeExpandedExonic.py		diff \| blob \| history
regionCounts.py		diff \| blob \| history
rnafarPairs.py		diff \| blob \| history
runRNAPairedAnalysis.py		diff \| blob \| history
runStandardAnalysis.py		diff \| blob \| history
runStrandedAnalysis.py		diff \| blob \| history
siteintersects.py		diff \| blob \| history
weighMultireads.py		diff \| blob \| history

ERANGE http://woldlab.caltech.edu/erange