GitHub - Walfred-MA/SegDupAnnotation

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 184 Commits
hmcnc @ 69e6400		hmcnc @ 69e6400
hmm		hmm
htslib @ 1830551		htslib @ 1830551
sedef @ d14abac		sedef @ d14abac
.gitmodules		.gitmodules
AddHeaderToSedef.py		AddHeaderToSedef.py
AlignIsoforms.sh		AlignIsoforms.sh
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
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
DivideBedToNonoverlappingIntervals.py		DivideBedToNonoverlappingIntervals.py
DivideFasta.py		DivideFasta.py
DuplicationTableToPairs.py		DuplicationTableToPairs.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
GEMBamToMask.cpp		GEMBamToMask.cpp
GetCoverageOfRegions.sh		GetCoverageOfRegions.sh
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
RemoveOriginal.py		RemoveOriginal.py
RemoveOriginalPAF.py		RemoveOriginalPAF.py
RemoveOverlappingGenes.py		RemoveOverlappingGenes.py
RemoveRedundantSubreads.py		RemoveRedundantSubreads.py
RenameFastaWithGenes.py		RenameFastaWithGenes.py
ReplaceChromName.py		ReplaceChromName.py
SedefDynamicMask.sh		SedefDynamicMask.sh
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
circos.conf		circos.conf
filter.subread.py		filter.subread.py
het_check.ini.py		het_check.ini.py
het_check.py		het_check.py
hmm_caller.vert.snakefile		hmm_caller.vert.snakefile
ref_hmm.snakefile		ref_hmm.snakefile
sedef.sh		sedef.sh

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.