GitHub - ChaissonLab/SegDupAnnotation

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 230 Commits
RepeatMasking		RepeatMasking
hmcnc @ ef8ae26		hmcnc @ ef8ae26
hmm		hmm
htslib @ c37e041		htslib @ c37e041
sedef @ d14abac		sedef @ d14abac
.gitmodules		.gitmodules
AddCoverageToBed.py		AddCoverageToBed.py
AddHeaderToSedef.py		AddHeaderToSedef.py
AlignIsoforms.sh		AlignIsoforms.sh
AnnotateCollapsesAndGenes.snakefile		AnnotateCollapsesAndGenes.snakefile
AnnotateOriginal.py		AnnotateOriginal.py
AnnotateWithTRF.py		AnnotateWithTRF.py
AppendCollapsedDupsList.py		AppendCollapsedDupsList.py
BamToCoverage.cpp		BamToCoverage.cpp
BamToFreq.cpp		BamToFreq.cpp
BamToFreq.sh		BamToFreq.sh
BamToMask.cpp		BamToMask.cpp
Bed12ToArcs.py		Bed12ToArcs.py
BedToCoverage.py		BedToCoverage.py
Cat.sh		Cat.sh
CollapsedDupsToName.py		CollapsedDupsToName.py
CombineCoverage.py		CombineCoverage.py
CombineMask.cpp		CombineMask.cpp
CombineMasked.py		CombineMasked.py
CombineTables.py		CombineTables.py
CombinedMasked.py		CombinedMasked.py
Compar2.sh		Compar2.sh
CountContig.cpp		CountContig.cpp
CountGenes.py		CountGenes.py
CountMasked.py		CountMasked.py
CountMaskedBed.py		CountMaskedBed.py
CountN.cpp		CountN.cpp
CountRep.cpp		CountRep.cpp
CountRep.py		CountRep.py
CountRepeatMasked.py		CountRepeatMasked.py
CountResolvedDuplicationMultiplicity.py		CountResolvedDuplicationMultiplicity.py
CovVcfToBed.py		CovVcfToBed.py
DivideBedToNonoverlappingIntervals.py		DivideBedToNonoverlappingIntervals.py
DivideFasta.py		DivideFasta.py
DuplicationTableToPairs.py		DuplicationTableToPairs.py
DupsToArcs.py		DupsToArcs.py
FilterBlacklist.py		FilterBlacklist.py
FilterIsoformsFromCollapse.py		FilterIsoformsFromCollapse.py
FilterLongestInOverlapSet.py		FilterLongestInOverlapSet.py
FilterMappedLength.py		FilterMappedLength.py
FilterMembersFromSameIsoformSet.py		FilterMembersFromSameIsoformSet.py
FilterPSL.py		FilterPSL.py
FilterSimilarLengths.py		FilterSimilarLengths.py
FilterTooMasked.py		FilterTooMasked.py
FindDuplicatedResolved.py		FindDuplicatedResolved.py
FixOriginalCopy.py		FixOriginalCopy.py
FractionCDSMapped.py		FractionCDSMapped.py
GEMBamToMask.cpp		GEMBamToMask.cpp
GetCoverageOfRegions.py		GetCoverageOfRegions.py
GetCoverageOfRegions.sh		GetCoverageOfRegions.sh
HardMask.cpp		HardMask.cpp
KeepNearFullLengthAlignments.py		KeepNearFullLengthAlignments.py
MakeDup.py		MakeDup.py
Makefile		Makefile
MapGeneToResolvedDup.sh		MapGeneToResolvedDup.sh
MaskBed.cpp		MaskBed.cpp
MaskedToBed.cpp		MaskedToBed.cpp
MeasureDepthOfResolvedDuplications.sh		MeasureDepthOfResolvedDuplications.sh
MergeIntervals.py		MergeIntervals.py
MultiMappedGenes.py		MultiMappedGenes.py
PairwiseAlignSedef.sh		PairwiseAlignSedef.sh
PlotIdeogram.R		PlotIdeogram.R
PrintBetweenGaps.py		PrintBetweenGaps.py
README.txt		README.txt
RefSeqToName.py		RefSeqToName.py
RemapRegion.sh		RemapRegion.sh
RemoveAnyOverlappingGenes.py		RemoveAnyOverlappingGenes.py
RemoveOriginal.py		RemoveOriginal.py
RemoveOriginalPAF.py		RemoveOriginalPAF.py
RemoveOverlappingGenes.py		RemoveOverlappingGenes.py
RemoveRedundantSubreads.py		RemoveRedundantSubreads.py
RenameFastaWithGenes.py		RenameFastaWithGenes.py
RepeatMaskGenome.snakefile		RepeatMaskGenome.snakefile
ReplaceChromName.py		ReplaceChromName.py
RunSedef.snakefile		RunSedef.snakefile
SedefDynamicMask.sh		SedefDynamicMask.sh
SegDupAnalysis.META.HPRC.snakefile		SegDupAnalysis.META.HPRC.snakefile
SegDupAnalysis.META.no_ref.snakefile		SegDupAnalysis.META.no_ref.snakefile
SegDupAnalysis.META.snakefile		SegDupAnalysis.META.snakefile
SegDupAnalysis.snakefile		SegDupAnalysis.snakefile
SelectDuplicationsFromMM2.py		SelectDuplicationsFromMM2.py
SeqToMer.py		SeqToMer.py
SimSizeMerge.py		SimSizeMerge.py
SimplifyName.py		SimplifyName.py
SimplifyNameInBed12.py		SimplifyNameInBed12.py
SplitCoverageBins.py		SplitCoverageBins.py
SplitFasta.py		SplitFasta.py
SplitSplicedGenes.py		SplitSplicedGenes.py
SplitToContig.cpp		SplitToContig.cpp
TRFToBed.py		TRFToBed.py
ToMer.cpp		ToMer.cpp
ToN.cpp		ToN.cpp
ToUpper.cpp		ToUpper.cpp
WriteNonOverlapping.py		WriteNonOverlapping.py
WriteNonOverlappingPairs.py		WriteNonOverlappingPairs.py

Repository files navigation

There are many files created by the analysis pipeline. Salient files are listed here:

Genes that overlap sequences counted as a duplication by Sedef:

genes_in_resolved_dups.one_isoform.bed

Only one isoform per gene is retained here. The first 12 columns are the gene in bed12 format. Columns 13-15 are the coordinates of the first duplication, and columns 16-18 are the copy of the duplication.