Last updated: 2020-04-29

Checks: 7 0

Knit directory: Comparative_APA/analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.6.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

The command set.seed(20190902) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    code/chimp_log/
    Ignored:    code/human_log/
    Ignored:    data/.DS_Store
    Ignored:    data/TrialFiltersMeta.txt.sb-9845453e-R58Y0Q/
    Ignored:    data/mediation_prot/
    Ignored:    data/metadata_HCpanel.txt.sb-284518db-RGf0kd/
    Ignored:    data/metadata_HCpanel.txt.sb-a5794dd2-i594qs/
    Ignored:    output/.DS_Store

Untracked files:
    Untracked:  ._.DS_Store
    Untracked:  Chimp/
    Untracked:  Human/
    Untracked:  analysis/AREstabilityScores.Rmd
    Untracked:  analysis/CrossChimpThreePrime.Rmd
    Untracked:  analysis/DiffTransProtvsExpression.Rmd
    Untracked:  analysis/DiffUsedUTR.Rmd
    Untracked:  analysis/GvizPlots.Rmd
    Untracked:  analysis/HandC.TvN
    Untracked:  analysis/PhenotypeOverlap10.Rmd
    Untracked:  analysis/annotationBias.Rmd
    Untracked:  analysis/assessReadQual.Rmd
    Untracked:  analysis/diffExpressionPantro6.Rmd
    Untracked:  code/._AlignmentScores.sh
    Untracked:  code/._BothFCMM.sh
    Untracked:  code/._BothFCMMPrim.sh
    Untracked:  code/._BothFCnewOInclusive.sh
    Untracked:  code/._ChimpStarMM2.sh
    Untracked:  code/._ClassifyLeafviz.sh
    Untracked:  code/._ClosestorthoEx.sh
    Untracked:  code/._Config_chimp.yaml
    Untracked:  code/._Config_chimp_full.yaml
    Untracked:  code/._Config_human.yaml
    Untracked:  code/._ConvertJunc2Bed.sh
    Untracked:  code/._CountNucleotides.py
    Untracked:  code/._CrossMapChimpRNA.sh
    Untracked:  code/._CrossMapThreeprime.sh
    Untracked:  code/._DiffSplice.sh
    Untracked:  code/._DiffSplicePlots.sh
    Untracked:  code/._DiffSplicePlots_gencode.sh
    Untracked:  code/._DiffSplice_gencode.sh
    Untracked:  code/._DiffSplice_removebad.sh
    Untracked:  code/._Filter255MM.sh
    Untracked:  code/._FilterPrimSec.sh
    Untracked:  code/._FindIntronForDomPAS.sh
    Untracked:  code/._FindIntronForDomPAS_DF.sh
    Untracked:  code/._GetMAPQscore.py
    Untracked:  code/._GetSecondaryMap.py
    Untracked:  code/._Lift5perPAS.sh
    Untracked:  code/._LiftFinalChimpJunc2Human.sh
    Untracked:  code/._LiftOrthoPAS2chimp.sh
    Untracked:  code/._MapBadSamples.sh
    Untracked:  code/._MismatchNumbers.sh
    Untracked:  code/._PAS_ATTAAA.sh
    Untracked:  code/._PAS_ATTAAA_df.sh
    Untracked:  code/._PAS_seqExpanded.sh
    Untracked:  code/._PASsequences.sh
    Untracked:  code/._PASsequences_DF.sh
    Untracked:  code/._PlotNuclearUsagebySpecies.R
    Untracked:  code/._PlotNuclearUsagebySpecies_DF.R
    Untracked:  code/._QuantMergedClusters.sh
    Untracked:  code/._RNATranscriptDTplot.sh
    Untracked:  code/._ReverseLiftFilter.R
    Untracked:  code/._RunFixLeafCluster.sh
    Untracked:  code/._RunNegMCMediation.sh
    Untracked:  code/._RunNegMCMediationDF.sh
    Untracked:  code/._RunPosMCMediationDF.err
    Untracked:  code/._RunPosMCMediationDF.sh
    Untracked:  code/._SAF2Bed.py
    Untracked:  code/._Snakefile
    Untracked:  code/._SnakefilePAS
    Untracked:  code/._SnakefilePASfilt
    Untracked:  code/._SortIndexBadSamples.sh
    Untracked:  code/._StarMM2.sh
    Untracked:  code/._TestFC.sh
    Untracked:  code/._assignPeak2Intronicregion
    Untracked:  code/._assignPeak2Intronicregion.sh
    Untracked:  code/._bed215upbed.py
    Untracked:  code/._bed2Bedbothstrand.py
    Untracked:  code/._bed2SAF_gen.py
    Untracked:  code/._buildIndecpantro5
    Untracked:  code/._buildIndecpantro5.sh
    Untracked:  code/._buildLeafviz.sh
    Untracked:  code/._buildLeafviz_leadAnno.sh
    Untracked:  code/._buildStarIndex.sh
    Untracked:  code/._chimpChromprder.sh
    Untracked:  code/._chimpMultiCov.sh
    Untracked:  code/._chimpMultiCov255.sh
    Untracked:  code/._chimpMultiCovInclusive.sh
    Untracked:  code/._chooseSignalSite.py
    Untracked:  code/._cleanbed2saf.py
    Untracked:  code/._cluster.json
    Untracked:  code/._cluster2bed.py
    Untracked:  code/._clusterLiftReverse.sh
    Untracked:  code/._clusterLiftReverse_removebad.sh
    Untracked:  code/._clusterLiftprimary.sh
    Untracked:  code/._clusterLiftprimary_removebad.sh
    Untracked:  code/._converBam2Junc.sh
    Untracked:  code/._converBam2Junc_removeBad.sh
    Untracked:  code/._extraSnakefiltpas
    Untracked:  code/._extractPhyloReg.py
    Untracked:  code/._extractPhyloRegGene.py
    Untracked:  code/._extractPhylopGeneral.ph
    Untracked:  code/._extractPhylopGeneral.py
    Untracked:  code/._extractPhylopReg200down.py
    Untracked:  code/._extractPhylopReg200up.py
    Untracked:  code/._filter5percPAS.py
    Untracked:  code/._filterNumChroms.py
    Untracked:  code/._filterPASforMP.py
    Untracked:  code/._filterPostLift.py
    Untracked:  code/._filterPrimaryread.py
    Untracked:  code/._filterSecondaryread.py
    Untracked:  code/._fixExonFC.py
    Untracked:  code/._fixFCheadforExp.py
    Untracked:  code/._fixLeafCluster.py
    Untracked:  code/._fixLiftedJunc.py
    Untracked:  code/._fixUTRexonanno.py
    Untracked:  code/._formathg38Anno.py
    Untracked:  code/._formatpantro6Anno.py
    Untracked:  code/._getRNAseqMapStats.sh
    Untracked:  code/._hg19MapStats.sh
    Untracked:  code/._humanChromorder.sh
    Untracked:  code/._humanMultiCov.sh
    Untracked:  code/._humanMultiCov255.sh
    Untracked:  code/._humanMultiCov_inclusive.sh
    Untracked:  code/._intersectLiftedPAS.sh
    Untracked:  code/._liftJunctionFiles.sh
    Untracked:  code/._liftPAS19to38.sh
    Untracked:  code/._liftedchimpJunc2human.sh
    Untracked:  code/._makeNuclearDapaplots.sh
    Untracked:  code/._makeNuclearDapaplots_DF.sh
    Untracked:  code/._makeSamplyGroupsHuman_TvN.py
    Untracked:  code/._mapRNAseqhg19.sh
    Untracked:  code/._mapRNAseqhg19_newPipeline.sh
    Untracked:  code/._maphg19.sh
    Untracked:  code/._maphg19_subjunc.sh
    Untracked:  code/._mediation_test.R
    Untracked:  code/._mergeChimp3prime_inhg38.sh
    Untracked:  code/._mergeandBWRNAseq.sh
    Untracked:  code/._mergedBam2BW.sh
    Untracked:  code/._nameClusters.py
    Untracked:  code/._negativeMediation_montecarlo.R
    Untracked:  code/._negativeMediation_montecarloDF.R
    Untracked:  code/._numMultimap.py
    Untracked:  code/._overlapMMandOrthoexon.sh
    Untracked:  code/._overlapPASandOrthoexon.sh
    Untracked:  code/._overlapapaQTLPAS.sh
    Untracked:  code/._parseHg38.py
    Untracked:  code/._postiveMediation_montecarlo_DF.R
    Untracked:  code/._prepareCleanLiftedFC_5perc4LC.py
    Untracked:  code/._prepareLeafvizAnno.sh
    Untracked:  code/._preparePAS4lift.py
    Untracked:  code/._primaryLift.sh
    Untracked:  code/._processhg38exons.py
    Untracked:  code/._quantJunc.sh
    Untracked:  code/._quantJunc_TEST.sh
    Untracked:  code/._quantJunc_removeBad.sh
    Untracked:  code/._quantLiftedPASPrimary.sh
    Untracked:  code/._quantMerged_seperatly.sh
    Untracked:  code/._recLiftchim2human.sh
    Untracked:  code/._revLiftPAShg38to19.sh
    Untracked:  code/._reverseLift.sh
    Untracked:  code/._runCheckReverseLift.sh
    Untracked:  code/._runChimpDiffIso.sh
    Untracked:  code/._runCountNucleotides.sh
    Untracked:  code/._runFilterNumChroms.sh
    Untracked:  code/._runHumanDiffIso.sh
    Untracked:  code/._runNuclearDiffIso_DF.sh
    Untracked:  code/._runNuclearDifffIso.sh
    Untracked:  code/._runTotalDiffIso.sh
    Untracked:  code/._run_chimpverifybam.sh
    Untracked:  code/._run_verifyBam.sh
    Untracked:  code/._snakemake.batch
    Untracked:  code/._snakemakePAS.batch
    Untracked:  code/._snakemakePASchimp.batch
    Untracked:  code/._snakemakePAShuman.batch
    Untracked:  code/._snakemake_chimp.batch
    Untracked:  code/._snakemake_human.batch
    Untracked:  code/._snakemakefiltPAS.batch
    Untracked:  code/._snakemakefiltPAS_chimp
    Untracked:  code/._snakemakefiltPAS_chimp.sh
    Untracked:  code/._snakemakefiltPAS_human.sh
    Untracked:  code/._spliceSite2Fasta.py
    Untracked:  code/._submit-snakemake-chimp.sh
    Untracked:  code/._submit-snakemake-human.sh
    Untracked:  code/._submit-snakemakePAS-chimp.sh
    Untracked:  code/._submit-snakemakePAS-human.sh
    Untracked:  code/._submit-snakemakefiltPAS-chimp.sh
    Untracked:  code/._submit-snakemakefiltPAS-human.sh
    Untracked:  code/._subset_diffisopheno_Nuclear_HvC.py
    Untracked:  code/._subset_diffisopheno_Nuclear_HvC_DF.py
    Untracked:  code/._subset_diffisopheno_Total_HvC.py
    Untracked:  code/._threeprimeOrthoFC.sh
    Untracked:  code/._transcriptDTplotsNuclear.sh
    Untracked:  code/._verifyBam4973.sh
    Untracked:  code/._verifyBam4973inHuman.sh
    Untracked:  code/._wrap_chimpverifybam.sh
    Untracked:  code/._wrap_verifyBam.sh
    Untracked:  code/._writeMergecode.py
    Untracked:  code/.snakemake/
    Untracked:  code/ALLPAS_sequenceDF.err
    Untracked:  code/ALLPAS_sequenceDF.out
    Untracked:  code/AlignmentScores.err
    Untracked:  code/AlignmentScores.out
    Untracked:  code/AlignmentScores.sh
    Untracked:  code/BothFCMM.err
    Untracked:  code/BothFCMM.out
    Untracked:  code/BothFCMM.sh
    Untracked:  code/BothFCMMPrim.err
    Untracked:  code/BothFCMMPrim.out
    Untracked:  code/BothFCMMPrim.sh
    Untracked:  code/BothFCnewOInclusive.sh
    Untracked:  code/BothFCnewOInclusive.sh.err
    Untracked:  code/BothFCnewOInclusive.sh.out
    Untracked:  code/ChimpStarMM2.err
    Untracked:  code/ChimpStarMM2.out
    Untracked:  code/ChimpStarMM2.sh
    Untracked:  code/ClassifyLeafviz.sh
    Untracked:  code/ClosestorthoEx.err
    Untracked:  code/ClosestorthoEx.out
    Untracked:  code/ClosestorthoEx.sh
    Untracked:  code/Config_chimp.yaml
    Untracked:  code/Config_chimp_full.yaml
    Untracked:  code/Config_human.yaml
    Untracked:  code/ConvertJunc2Bed.err
    Untracked:  code/ConvertJunc2Bed.out
    Untracked:  code/ConvertJunc2Bed.sh
    Untracked:  code/CountNucleotides.py
    Untracked:  code/CrossMapChimpRNA.sh
    Untracked:  code/CrossMapThreeprime.sh
    Untracked:  code/CrossmapChimp3prime.err
    Untracked:  code/CrossmapChimp3prime.out
    Untracked:  code/CrossmapChimpRNA.err
    Untracked:  code/CrossmapChimpRNA.out
    Untracked:  code/DTUTR.sh
    Untracked:  code/DiffSplice.err
    Untracked:  code/DiffSplice.out
    Untracked:  code/DiffSplice.sh
    Untracked:  code/DiffSplicePlots.err
    Untracked:  code/DiffSplicePlots.out
    Untracked:  code/DiffSplicePlots.sh
    Untracked:  code/DiffSplicePlots_gencode.sh
    Untracked:  code/DiffSplice_gencode.sh
    Untracked:  code/DiffSplice_removebad.err
    Untracked:  code/DiffSplice_removebad.out
    Untracked:  code/DiffSplice_removebad.sh
    Untracked:  code/Filter255.err
    Untracked:  code/Filter255.out
    Untracked:  code/Filter255MM.sh
    Untracked:  code/FilterPrimSec.err
    Untracked:  code/FilterPrimSec.out
    Untracked:  code/FilterPrimSec.sh
    Untracked:  code/FilterReverseLift.err
    Untracked:  code/FilterReverseLift.out
    Untracked:  code/FindDomXCutoff.py
    Untracked:  code/FindIntronForDomPAS.err
    Untracked:  code/FindIntronForDomPAS.out
    Untracked:  code/FindIntronForDomPAS.sh
    Untracked:  code/FindIntronForDomPAS_DF.sh
    Untracked:  code/GencodeDiffSplice.err
    Untracked:  code/GencodeDiffSplice.out
    Untracked:  code/GetMAPQscore.py
    Untracked:  code/GetSecondaryMap.py
    Untracked:  code/GetTopminus2Usage.py
    Untracked:  code/H3K36me3DTplot.err
    Untracked:  code/H3K36me3DTplot.out
    Untracked:  code/H3K36me3DTplot.sh
    Untracked:  code/H3K36me3DTplot_DiffIso.err
    Untracked:  code/H3K36me3DTplot_DiffIso.out
    Untracked:  code/H3K36me3DTplot_DiffIso.sh
    Untracked:  code/H3K36me3DTplot_Specific.err
    Untracked:  code/H3K36me3DTplot_Specific.out
    Untracked:  code/H3K36me3DTplot_Specific.sh
    Untracked:  code/H3K36me3DTplot_distalPAS.err
    Untracked:  code/H3K36me3DTplot_distalPAS.out
    Untracked:  code/H3K36me3DTplot_distalPAS.sh
    Untracked:  code/H3K36me3DTplot_transcript.err
    Untracked:  code/H3K36me3DTplot_transcript.out
    Untracked:  code/H3K36me3DTplot_transcript.sh
    Untracked:  code/H3K36me3DTplotwide.err
    Untracked:  code/H3K36me3DTplotwide.out
    Untracked:  code/H3K36me3DTplotwide.sh
    Untracked:  code/H3K9me3DTplot_transcript.err
    Untracked:  code/H3K9me3DTplot_transcript.out
    Untracked:  code/H3K9me3DTplot_transcript.sh
    Untracked:  code/H3K9me3_processandDT.sh
    Untracked:  code/HchromOrder.err
    Untracked:  code/HchromOrder.out
    Untracked:  code/InfoContentShannon.py
    Untracked:  code/IntersectMMandOrtho.err
    Untracked:  code/IntersectMMandOrtho.out
    Untracked:  code/IntersectPASandOrtho.err
    Untracked:  code/IntersectPASandOrtho.out
    Untracked:  code/JunctionLift.err
    Untracked:  code/JunctionLift.out
    Untracked:  code/JunctionLiftFinalChimp.err
    Untracked:  code/JunctionLiftFinalChimp.out
    Untracked:  code/Lift5perPAS.sh
    Untracked:  code/Lift5perPASbed.err
    Untracked:  code/Lift5perPASbed.out
    Untracked:  code/LiftClustersFirst.err
    Untracked:  code/LiftClustersFirst.out
    Untracked:  code/LiftClustersFirst_remove.err
    Untracked:  code/LiftClustersFirst_remove.out
    Untracked:  code/LiftClustersSecond.err
    Untracked:  code/LiftClustersSecond.out
    Untracked:  code/LiftClustersSecond_remove.err
    Untracked:  code/LiftClustersSecond_remove.out
    Untracked:  code/LiftFinalChimpJunc2Human.sh
    Untracked:  code/LiftOrthoPAS2chimp.sh
    Untracked:  code/LiftorthoPAS.err
    Untracked:  code/LiftorthoPASt.out
    Untracked:  code/Log.out
    Untracked:  code/MapBadSamples.err
    Untracked:  code/MapBadSamples.out
    Untracked:  code/MapBadSamples.sh
    Untracked:  code/MapStats.err
    Untracked:  code/MapStats.out
    Untracked:  code/MaxEntCode/
    Untracked:  code/MergeClusters.err
    Untracked:  code/MergeClusters.out
    Untracked:  code/MergeClusters.sh
    Untracked:  code/MismatchNumbers.err
    Untracked:  code/MismatchNumbers.out
    Untracked:  code/MismatchNumbers.sh
    Untracked:  code/NuclearDTUTR.err
    Untracked:  code/NuclearDTUTRt.out
    Untracked:  code/NuclearPlotsDEandDiffDom_4.err
    Untracked:  code/NuclearPlotsDEandDiffDom_4.out
    Untracked:  code/NuclearPlotsDEandDiffDom_4.sh
    Untracked:  code/PAS_ATTAAA.err
    Untracked:  code/PAS_ATTAAA.out
    Untracked:  code/PAS_ATTAAA.sh
    Untracked:  code/PAS_ATTAAADF.err
    Untracked:  code/PAS_ATTAAADF.out
    Untracked:  code/PAS_ATTAAA_df.sh
    Untracked:  code/PAS_seqExpanded.sh
    Untracked:  code/PAS_sequence.err
    Untracked:  code/PAS_sequence.out
    Untracked:  code/PAS_sequenceDF.err
    Untracked:  code/PAS_sequenceDF.out
    Untracked:  code/PASexpanded_sequenceDF.err
    Untracked:  code/PASexpanded_sequenceDF.out
    Untracked:  code/PASsequences.sh
    Untracked:  code/PASsequences_DF.sh
    Untracked:  code/PlotNuclearUsagebySpecies.R
    Untracked:  code/PlotNuclearUsagebySpecies_DF.R
    Untracked:  code/PlotNuclearUsagebySpecies_DF_DEout.R
    Untracked:  code/QuantMergeClusters
    Untracked:  code/QuantMergeClusters.err
    Untracked:  code/QuantMergeClusters.out
    Untracked:  code/QuantMergedClusters.sh
    Untracked:  code/RNATranscriptDTplot.err
    Untracked:  code/RNATranscriptDTplot.out
    Untracked:  code/RNATranscriptDTplot.sh
    Untracked:  code/Rev_liftoverPAShg19to38.err
    Untracked:  code/Rev_liftoverPAShg19to38.out
    Untracked:  code/ReverseLiftFilter.R
    Untracked:  code/RunFixCluster.err
    Untracked:  code/RunFixCluster.out
    Untracked:  code/RunFixLeafCluster.sh
    Untracked:  code/RunNegMCMediation.err
    Untracked:  code/RunNegMCMediation.sh
    Untracked:  code/RunNegMCMediationDF.err
    Untracked:  code/RunNegMCMediationDF.out
    Untracked:  code/RunNegMCMediationDF.sh
    Untracked:  code/RunNegMCMediationr.out
    Untracked:  code/RunNewDom.err
    Untracked:  code/RunNewDom.out
    Untracked:  code/RunPosMCMediation.err
    Untracked:  code/RunPosMCMediation.sh
    Untracked:  code/RunPosMCMediationDF.err
    Untracked:  code/RunPosMCMediationDF.out
    Untracked:  code/RunPosMCMediationDF.sh
    Untracked:  code/RunPosMCMediationr.out
    Untracked:  code/SAF215upbed_gen.py
    Untracked:  code/SAF2Bed.py
    Untracked:  code/Snakefile
    Untracked:  code/SnakefilePAS
    Untracked:  code/SnakefilePASfilt
    Untracked:  code/SortIndexBadSamples.err
    Untracked:  code/SortIndexBadSamples.out
    Untracked:  code/SortIndexBadSamples.sh
    Untracked:  code/StarMM2.err
    Untracked:  code/StarMM2.out
    Untracked:  code/StarMM2.sh
    Untracked:  code/TestFC.err
    Untracked:  code/TestFC.out
    Untracked:  code/TestFC.sh
    Untracked:  code/TotalTranscriptDTplot.err
    Untracked:  code/TotalTranscriptDTplot.out
    Untracked:  code/UTR2FASTA.py
    Untracked:  code/Upstream10Bases_general.py
    Untracked:  code/allPASSeq_df.sh
    Untracked:  code/apaQTLsnake.err
    Untracked:  code/apaQTLsnake.out
    Untracked:  code/apaQTLsnakePAS.err
    Untracked:  code/apaQTLsnakePAS.out
    Untracked:  code/apaQTLsnakePAShuman.err
    Untracked:  code/apaQTLsnakefiltPAS.err
    Untracked:  code/apaQTLsnakefiltPAS.out
    Untracked:  code/assignPeak2Intronicregion.err
    Untracked:  code/assignPeak2Intronicregion.out
    Untracked:  code/assignPeak2Intronicregion.sh
    Untracked:  code/bam2junc.err
    Untracked:  code/bam2junc.out
    Untracked:  code/bam2junc_remove.err
    Untracked:  code/bam2junc_remove.out
    Untracked:  code/bed215upbed.py
    Untracked:  code/bed2Bedbothstrand.py
    Untracked:  code/bed2SAF_gen.py
    Untracked:  code/bed2saf.py
    Untracked:  code/bg_to_cov.py
    Untracked:  code/buildIndecpantro5
    Untracked:  code/buildIndecpantro5.sh
    Untracked:  code/buildLeafviz.err
    Untracked:  code/buildLeafviz.out
    Untracked:  code/buildLeafviz.sh
    Untracked:  code/buildLeafviz_leadAnno.sh
    Untracked:  code/buildLeafviz_leafanno.err
    Untracked:  code/buildLeafviz_leafanno.out
    Untracked:  code/buildStarIndex.sh
    Untracked:  code/callPeaksYL.py
    Untracked:  code/chimpChromprder.sh
    Untracked:  code/chimpMultiCov.err
    Untracked:  code/chimpMultiCov.out
    Untracked:  code/chimpMultiCov.sh
    Untracked:  code/chimpMultiCov255.sh
    Untracked:  code/chimpMultiCovInclusive.err
    Untracked:  code/chimpMultiCovInclusive.out
    Untracked:  code/chimpMultiCovInclusive.sh
    Untracked:  code/chooseAnno2Bed.py
    Untracked:  code/chooseAnno2SAF.py
    Untracked:  code/chooseSignalSite.py
    Untracked:  code/chromOrder.err
    Untracked:  code/chromOrder.out
    Untracked:  code/classifyLeafviz.err
    Untracked:  code/classifyLeafviz.out
    Untracked:  code/cleanbed2saf.py
    Untracked:  code/cluster.json
    Untracked:  code/cluster2bed.py
    Untracked:  code/clusterLiftReverse.sh
    Untracked:  code/clusterLiftReverse_removebad.sh
    Untracked:  code/clusterLiftprimary.sh
    Untracked:  code/clusterLiftprimary_removebad.sh
    Untracked:  code/clusterPAS.json
    Untracked:  code/clusterfiltPAS.json
    Untracked:  code/comands2Mege.sh
    Untracked:  code/converBam2Junc.sh
    Untracked:  code/converBam2Junc_removeBad.sh
    Untracked:  code/convertNumeric.py
    Untracked:  code/environment.yaml
    Untracked:  code/extraSnakefiltpas
    Untracked:  code/extractPhyloReg.py
    Untracked:  code/extractPhyloRegGene.py
    Untracked:  code/extractPhylopGeneral.py
    Untracked:  code/extractPhylopReg200down.py
    Untracked:  code/extractPhylopReg200up.py
    Untracked:  code/filter5perc.R
    Untracked:  code/filter5percPAS.py
    Untracked:  code/filter5percPheno.py
    Untracked:  code/filterBamforMP.pysam2_gen.py
    Untracked:  code/filterJuncChroms.err
    Untracked:  code/filterJuncChroms.out
    Untracked:  code/filterMissprimingInNuc10_gen.py
    Untracked:  code/filterNumChroms.py
    Untracked:  code/filterPASforMP.py
    Untracked:  code/filterPostLift.py
    Untracked:  code/filterPrimaryread.py
    Untracked:  code/filterSAFforMP_gen.py
    Untracked:  code/filterSecondaryread.py
    Untracked:  code/filterSortBedbyCleanedBed_gen.R
    Untracked:  code/filterpeaks.py
    Untracked:  code/fixExonFC.py
    Untracked:  code/fixFChead.py
    Untracked:  code/fixFChead_bothfrac.py
    Untracked:  code/fixFCheadforExp.py
    Untracked:  code/fixLeafCluster.py
    Untracked:  code/fixLiftedJunc.py
    Untracked:  code/fixUTRexonanno.py
    Untracked:  code/formathg38Anno.py
    Untracked:  code/generateStarIndex.err
    Untracked:  code/generateStarIndex.out
    Untracked:  code/generateStarIndexHuman.err
    Untracked:  code/generateStarIndexHuman.out
    Untracked:  code/getAlloverlap.py
    Untracked:  code/getRNAseqMapStats.sh
    Untracked:  code/hg19MapStats.err
    Untracked:  code/hg19MapStats.out
    Untracked:  code/hg19MapStats.sh
    Untracked:  code/humanChromorder.sh
    Untracked:  code/humanFiles
    Untracked:  code/humanMultiCov.err
    Untracked:  code/humanMultiCov.out
    Untracked:  code/humanMultiCov.sh
    Untracked:  code/humanMultiCov255.err
    Untracked:  code/humanMultiCov255.out
    Untracked:  code/humanMultiCov255.sh
    Untracked:  code/humanMultiCovInclusive.err
    Untracked:  code/humanMultiCovInclusive.out
    Untracked:  code/humanMultiCov_inclusive.sh
    Untracked:  code/infoContentSimpson.py
    Untracked:  code/intersectAnno.err
    Untracked:  code/intersectAnno.out
    Untracked:  code/intersectAnnoExt.err
    Untracked:  code/intersectAnnoExt.out
    Untracked:  code/intersectLiftedPAS.sh
    Untracked:  code/leafcutter_merge_regtools_redo.py
    Untracked:  code/liftJunctionFiles.sh
    Untracked:  code/liftPAS19to38.sh
    Untracked:  code/liftoverPAShg19to38.err
    Untracked:  code/liftoverPAShg19to38.out
    Untracked:  code/log/
    Untracked:  code/make5percPeakbed.py
    Untracked:  code/makeFileID.py
    Untracked:  code/makeNuclearDapaplots.sh
    Untracked:  code/makeNuclearDapaplots_DF.sh
    Untracked:  code/makeNuclearPlots.err
    Untracked:  code/makeNuclearPlots.out
    Untracked:  code/makeNuclearPlotsDF.err
    Untracked:  code/makeNuclearPlotsDF.out
    Untracked:  code/makePheno.py
    Untracked:  code/makeSamplyGroupsChimp_TvN.py
    Untracked:  code/makeSamplyGroupsHuman_TvN.py
    Untracked:  code/mapRNAseqhg19.sh
    Untracked:  code/mapRNAseqhg19_newPipeline.sh
    Untracked:  code/maphg19.err
    Untracked:  code/maphg19.out
    Untracked:  code/maphg19.sh
    Untracked:  code/maphg19_new.err
    Untracked:  code/maphg19_new.out
    Untracked:  code/maphg19_sub.err
    Untracked:  code/maphg19_sub.out
    Untracked:  code/maphg19_subjunc.sh
    Untracked:  code/mediation_test.R
    Untracked:  code/merge.err
    Untracked:  code/mergeChimp3prime_inhg38.sh
    Untracked:  code/mergeChimpRNA.sh
    Untracked:  code/merge_leafcutter_clusters_redo.py
    Untracked:  code/mergeandBWRNAseq.sh
    Untracked:  code/mergeandsort_ChimpinHuman.err
    Untracked:  code/mergeandsort_ChimpinHuman.out
    Untracked:  code/mergeandsort_H3K9me3
    Untracked:  code/mergeandsort_h3k36me3
    Untracked:  code/mergeandsorth3k36me3.sh
    Untracked:  code/mergedBam2BW.sh
    Untracked:  code/mergedbam2bw.err
    Untracked:  code/mergedbam2bw.out
    Untracked:  code/mergedbamRNAand2bw.err
    Untracked:  code/mergedbamRNAand2bw.out
    Untracked:  code/nameClusters.py
    Untracked:  code/namePeaks.py
    Untracked:  code/negativeMediation_montecarlo.R
    Untracked:  code/negativeMediation_montecarloDF.R
    Untracked:  code/nuclearTranscriptDTplot.err
    Untracked:  code/nuclearTranscriptDTplot.out
    Untracked:  code/numMultimap.py
    Untracked:  code/overlapMMandOrthoexon.sh
    Untracked:  code/overlapPAS.err
    Untracked:  code/overlapPAS.out
    Untracked:  code/overlapPASandOrthoexon.sh
    Untracked:  code/overlapapaQTLPAS.sh
    Untracked:  code/overlapapaQTLPAS_extended.sh
    Untracked:  code/overlapapaQTLPAS_samples.sh
    Untracked:  code/parseHg38.py
    Untracked:  code/peak2PAS.py
    Untracked:  code/pheno2countonly.R
    Untracked:  code/postiveMediation_montecarlo.R
    Untracked:  code/postiveMediation_montecarlo_DF.R
    Untracked:  code/prepareAnnoLeafviz.err
    Untracked:  code/prepareAnnoLeafviz.out
    Untracked:  code/prepareCleanLiftedFC_5perc4LC.py
    Untracked:  code/prepareLeafvizAnno.sh
    Untracked:  code/preparePAS4lift.py
    Untracked:  code/prepare_phenotype_table.py
    Untracked:  code/primaryLift.err
    Untracked:  code/primaryLift.out
    Untracked:  code/primaryLift.sh
    Untracked:  code/processhg38exons.py
    Untracked:  code/quantJunc.sh
    Untracked:  code/quantJunc_TEST.sh
    Untracked:  code/quantJunc_removeBad.sh
    Untracked:  code/quantLiftedPAS.err
    Untracked:  code/quantLiftedPAS.out
    Untracked:  code/quantLiftedPAS.sh
    Untracked:  code/quantLiftedPASPrimary.err
    Untracked:  code/quantLiftedPASPrimary.out
    Untracked:  code/quantLiftedPASPrimary.sh
    Untracked:  code/quatJunc.err
    Untracked:  code/quatJunc.out
    Untracked:  code/recChimpback2Human.err
    Untracked:  code/recChimpback2Human.out
    Untracked:  code/recLiftchim2human.sh
    Untracked:  code/revLift.err
    Untracked:  code/revLift.out
    Untracked:  code/revLiftPAShg38to19.sh
    Untracked:  code/reverseLift.sh
    Untracked:  code/runCheckReverseLift.sh
    Untracked:  code/runChimpDiffIso.sh
    Untracked:  code/runChimpDiffIsoDF.sh
    Untracked:  code/runCountNucleotides.err
    Untracked:  code/runCountNucleotides.out
    Untracked:  code/runCountNucleotides.sh
    Untracked:  code/runCountNucleotidesPantro6.err
    Untracked:  code/runCountNucleotidesPantro6.out
    Untracked:  code/runCountNucleotides_pantro6.sh
    Untracked:  code/runFilterNumChroms.sh
    Untracked:  code/runHumanDiffIso.sh
    Untracked:  code/runHumanDiffIsoDF.sh
    Untracked:  code/runNewDom.sh
    Untracked:  code/runNuclearDiffIso_DF.sh
    Untracked:  code/runNuclearDifffIso.sh
    Untracked:  code/runTotalDiffIso.sh
    Untracked:  code/run_Chimpleafcutter_ds.err
    Untracked:  code/run_Chimpleafcutter_ds.out
    Untracked:  code/run_Chimpverifybam.err
    Untracked:  code/run_Chimpverifybam.out
    Untracked:  code/run_Humanleafcutter_dF.err
    Untracked:  code/run_Humanleafcutter_dF.out
    Untracked:  code/run_Humanleafcutter_ds.err
    Untracked:  code/run_Humanleafcutter_ds.out
    Untracked:  code/run_Nuclearleafcutter_ds.err
    Untracked:  code/run_Nuclearleafcutter_ds.out
    Untracked:  code/run_Nuclearleafcutter_dsDF.err
    Untracked:  code/run_Nuclearleafcutter_dsDF.out
    Untracked:  code/run_Totalleafcutter_ds.err
    Untracked:  code/run_Totalleafcutter_ds.out
    Untracked:  code/run_chimpverifybam.sh
    Untracked:  code/run_verifyBam.sh
    Untracked:  code/run_verifybam.err
    Untracked:  code/run_verifybam.out
    Untracked:  code/slurm-62824013.out
    Untracked:  code/slurm-62825841.out
    Untracked:  code/slurm-62826116.out
    Untracked:  code/slurm-64108209.out
    Untracked:  code/slurm-64108521.out
    Untracked:  code/slurm-64108557.out
    Untracked:  code/snakePASChimp.err
    Untracked:  code/snakePASChimp.out
    Untracked:  code/snakePAShuman.out
    Untracked:  code/snakemake.batch
    Untracked:  code/snakemakeChimp.err
    Untracked:  code/snakemakeChimp.out
    Untracked:  code/snakemakeHuman.err
    Untracked:  code/snakemakeHuman.out
    Untracked:  code/snakemakePAS.batch
    Untracked:  code/snakemakePASFiltChimp.err
    Untracked:  code/snakemakePASFiltChimp.out
    Untracked:  code/snakemakePASFiltHuman.err
    Untracked:  code/snakemakePASFiltHuman.out
    Untracked:  code/snakemakePAS_Human.batch
    Untracked:  code/snakemakePASchimp.batch
    Untracked:  code/snakemakePAShuman.batch
    Untracked:  code/snakemake_chimp.batch
    Untracked:  code/snakemake_human.batch
    Untracked:  code/snakemakefiltPAS.batch
    Untracked:  code/snakemakefiltPAS_chimp.sh
    Untracked:  code/snakemakefiltPAS_human.batch
    Untracked:  code/snakemakefiltPAS_human.sh
    Untracked:  code/spliceSite2Fasta.py
    Untracked:  code/submit-snakemake-chimp.sh
    Untracked:  code/submit-snakemake-human.sh
    Untracked:  code/submit-snakemakePAS-chimp.sh
    Untracked:  code/submit-snakemakePAS-human.sh
    Untracked:  code/submit-snakemakefiltPAS-chimp.sh
    Untracked:  code/submit-snakemakefiltPAS-human.sh
    Untracked:  code/subset_diffisopheno.py
    Untracked:  code/subset_diffisopheno_Chimp_tvN.py
    Untracked:  code/subset_diffisopheno_Chimp_tvN_DF.py
    Untracked:  code/subset_diffisopheno_Huma_tvN.py
    Untracked:  code/subset_diffisopheno_Huma_tvN_DF.py
    Untracked:  code/subset_diffisopheno_Nuclear_HvC.py
    Untracked:  code/subset_diffisopheno_Nuclear_HvC_DF.py
    Untracked:  code/subset_diffisopheno_Total_HvC.py
    Untracked:  code/test
    Untracked:  code/test.txt
    Untracked:  code/threeprimeOrthoFC.out
    Untracked:  code/threeprimeOrthoFC.sh
    Untracked:  code/threeprimeOrthoFCcd.err
    Untracked:  code/transcriptDTplotsNuclear.sh
    Untracked:  code/transcriptDTplotsTotal.sh
    Untracked:  code/verifyBam4973.sh
    Untracked:  code/verifyBam4973inHuman.sh
    Untracked:  code/verifybam4973.err
    Untracked:  code/verifybam4973.out
    Untracked:  code/verifybam4973HumanMap.err
    Untracked:  code/verifybam4973HumanMap.out
    Untracked:  code/wrap_Chimpverifybam.err
    Untracked:  code/wrap_Chimpverifybam.out
    Untracked:  code/wrap_chimpverifybam.sh
    Untracked:  code/wrap_verifyBam.sh
    Untracked:  code/wrap_verifybam.err
    Untracked:  code/wrap_verifybam.out
    Untracked:  code/writeMergecode.py
    Untracked:  data/._.DS_Store
    Untracked:  data/._HC_filenames.txt
    Untracked:  data/._HC_filenames.txt.sb-4426323c-IKIs0S
    Untracked:  data/._HC_filenames.xlsx
    Untracked:  data/._MapPantro6_meta.txt
    Untracked:  data/._MapPantro6_meta.txt.sb-a5794dd2-Cskmlm
    Untracked:  data/._MapPantro6_meta.xlsx
    Untracked:  data/._OppositeSpeciesMap.txt
    Untracked:  data/._OppositeSpeciesMap.txt.sb-a5794dd2-mayWJf
    Untracked:  data/._OppositeSpeciesMap.xlsx
    Untracked:  data/._RNASEQ_metadata.txt
    Untracked:  data/._RNASEQ_metadata.txt.sb-4426323c-TE4ns3
    Untracked:  data/._RNASEQ_metadata.txt.sb-51f67ae1-HXp7Gq
    Untracked:  data/._RNASEQ_metadata_2Removed.txt
    Untracked:  data/._RNASEQ_metadata_2Removed.txt.sb-4426323c-a4lBwx
    Untracked:  data/._RNASEQ_metadata_2Removed.xlsx
    Untracked:  data/._RNASEQ_metadata_stranded.txt
    Untracked:  data/._RNASEQ_metadata_stranded.txt.sb-a5794dd2-D659m2
    Untracked:  data/._RNASEQ_metadata_stranded.txt.sb-a5794dd2-ImNMoY
    Untracked:  data/._RNASEQ_metadata_stranded.txt.sb-e4bf31f0-ZGnGgl
    Untracked:  data/._RNASEQ_metadata_stranded.xlsx
    Untracked:  data/._TrialFiltersMeta.txt
    Untracked:  data/._TrialFiltersMeta.txt.sb-9845453e-R58Y0Q
    Untracked:  data/._metadata_HCpanel.txt
    Untracked:  data/._metadata_HCpanel.txt.sb-a3d92a2d-b9cYoF
    Untracked:  data/._metadata_HCpanel.txt.sb-a5794dd2-i594qs
    Untracked:  data/._metadata_HCpanel.txt.sb-f4823d1e-qihGek
    Untracked:  data/._metadata_HCpanel_frompantro5.xlsx
    Untracked:  data/._~$RNASEQ_metadata.xlsx
    Untracked:  data/._~$metadata_HCpanel.xlsx
    Untracked:  data/._.xlsx
    Untracked:  data/AREelements/
    Untracked:  data/BaseComp/
    Untracked:  data/CleanLiftedPeaks_FC_primary/
    Untracked:  data/CompapaQTLpas/
    Untracked:  data/DNDS/
    Untracked:  data/DTmatrix/
    Untracked:  data/DiffDomandDE_example/
    Untracked:  data/DiffExpression/
    Untracked:  data/DiffIso_Nuclear/
    Untracked:  data/DiffIso_Nuclear_DF/
    Untracked:  data/DiffIso_Total/
    Untracked:  data/DiffSplice/
    Untracked:  data/DiffSplice_liftedJunc/
    Untracked:  data/DiffSplice_removeBad/
    Untracked:  data/DomDefGreaterX/
    Untracked:  data/DomStructure_4/
    Untracked:  data/DominantPAS/
    Untracked:  data/DominantPAS_DF/
    Untracked:  data/EvalPantro5/
    Untracked:  data/H3K36me3/
    Untracked:  data/HC_filenames.txt
    Untracked:  data/HC_filenames.xlsx
    Untracked:  data/HumanMolPheno/
    Untracked:  data/InfoContent/
    Untracked:  data/Khan_prot/
    Untracked:  data/Li_eqtls/
    Untracked:  data/MapPantro6_meta.txt
    Untracked:  data/MapPantro6_meta.xlsx
    Untracked:  data/MapStats/
    Untracked:  data/NormalizedClusters/
    Untracked:  data/NuclearHvC/
    Untracked:  data/NuclearHvC_DF/
    Untracked:  data/OppositeSpeciesMap.txt
    Untracked:  data/OppositeSpeciesMap.xlsx
    Untracked:  data/OrthoExonBed/
    Untracked:  data/OverlapBenchmark/
    Untracked:  data/OverlappingPAS/
    Untracked:  data/PAS/
    Untracked:  data/PAS_SAF/
    Untracked:  data/PAS_doubleFilter/
    Untracked:  data/Peaks_5perc/
    Untracked:  data/Pheno_5perc/
    Untracked:  data/Pheno_5perc_DF_nuclear/
    Untracked:  data/Pheno_5perc_nuclear/
    Untracked:  data/Pheno_5perc_nuclear_old/
    Untracked:  data/Pheno_5perc_total/
    Untracked:  data/PhyloP/
    Untracked:  data/Pol2Chip/
    Untracked:  data/RNASEQ_metadata.txt
    Untracked:  data/RNASEQ_metadata_2Removed.txt
    Untracked:  data/RNASEQ_metadata_2Removed.xlsx
    Untracked:  data/RNASEQ_metadata_stranded.txt
    Untracked:  data/RNASEQ_metadata_stranded.txt.sb-e4bf31f0-ZGnGgl/
    Untracked:  data/RNASEQ_metadata_stranded.xlsx
    Untracked:  data/SignalSites/
    Untracked:  data/SignalSites_doublefilter/
    Untracked:  data/SpliceSite/
    Untracked:  data/TestAnnoBiasOE/
    Untracked:  data/TestMM2/
    Untracked:  data/TestMM2_AS/
    Untracked:  data/TestMM2_PrimaryRead/
    Untracked:  data/TestMM2_SeondaryRead/
    Untracked:  data/TestMM2_mismatch/
    Untracked:  data/TestMM2_quality/
    Untracked:  data/TestWithinMergePAS/
    Untracked:  data/Test_FC_methods/
    Untracked:  data/Threeprime2Ortho/
    Untracked:  data/TotalFractionPAS/
    Untracked:  data/TotalHvC/
    Untracked:  data/TrialFiltersMeta.txt
    Untracked:  data/TwoBadSampleAnalysis/
    Untracked:  data/Wang_ribo/
    Untracked:  data/apaQTLGenes/
    Untracked:  data/bioGRID/
    Untracked:  data/chainFiles/
    Untracked:  data/cleanPeaks_anno/
    Untracked:  data/cleanPeaks_byspecies/
    Untracked:  data/cleanPeaks_lifted/
    Untracked:  data/files4viz_nuclear/
    Untracked:  data/files4viz_nuclear_DF/
    Untracked:  data/gviz/
    Untracked:  data/leafviz/
    Untracked:  data/liftover_files/
    Untracked:  data/mediation/
    Untracked:  data/mediation_DF/
    Untracked:  data/metadata_HCpanel.txt
    Untracked:  data/metadata_HCpanel.xlsx
    Untracked:  data/metadata_HCpanel_extra.txt
    Untracked:  data/metadata_HCpanel_frompantro5.txt
    Untracked:  data/metadata_HCpanel_frompantro5.xlsx
    Untracked:  data/miRNA/
    Untracked:  data/multimap/
    Untracked:  data/orthoUTR/
    Untracked:  data/paiDecay/
    Untracked:  data/primaryLift/
    Untracked:  data/reverseLift/
    Untracked:  data/testQuant/
    Untracked:  data/~$RNASEQ_metadata.xlsx
    Untracked:  data/~$metadata_HCpanel.xlsx
    Untracked:  data/.xlsx
    Untracked:  output/._.DS_Store
    Untracked:  output/dAPAandDomEnrich.png
    Untracked:  output/dEandDomEnrich.png
    Untracked:  output/dtPlots/
    Untracked:  projectNotes.Rmd
    Untracked:  proteinModelSet.Rmd

Unstaged changes:
    Modified:   analysis/DeandNumPAS.Rmd
    Modified:   analysis/DiffTop2SecondDom.Rmd
    Modified:   analysis/ExploredAPA.Rmd
    Modified:   analysis/ExploredAPA_DF.Rmd
    Modified:   analysis/MMExpreiment.Rmd
    Modified:   analysis/OppositeMap.Rmd
    Modified:   analysis/PTM_analysis.Rmd
    Modified:   analysis/TotalDomStructure.Rmd
    Modified:   analysis/TotalVNuclearBothSpecies.Rmd
    Modified:   analysis/annotationInfo.Rmd
    Modified:   analysis/changeMisprimcut.Rmd
    Modified:   analysis/comp2apaQTLPAS.Rmd
    Modified:   analysis/correlationPhenos.Rmd
    Modified:   analysis/establishCutoffs.Rmd
    Modified:   analysis/investigatePantro5.Rmd
    Modified:   analysis/mRNADecay.Rmd
    Modified:   analysis/multiMap.Rmd
    Modified:   analysis/pol2.Rmd
    Modified:   analysis/signalsites_doublefilter.Rmd
    Modified:   analysis/speciesSpecific.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.


These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
Rmd 19a855b brimittleman 2020-04-29 hist mark plots and info with vars
html fa67b41 brimittleman 2020-04-28 Build site.
Rmd e51455f brimittleman 2020-04-28 add h3 and info with other vars

library(tidyverse)
── Attaching packages ────────────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.1       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.3.1  
✔ readr   1.3.1       ✔ forcats 0.3.0  
── Conflicts ───────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

general enrichment

H3K36me3 is a mark associated with active transcription. I will see if this mark is different based on conservation of apa.

I will start by downloading data from encode for the LCLs. I will work with bam files so I can make deep tools plots and see if there is coverage at PAS.

mkdir ../data/H3K36me3

Merge, sort, index these to use with deep tools.

mergeandsorth3k36me3.sh

#!/bin/bash

#SBATCH --job-name=mergeandsort_h3k36me3
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=mergeandsort_h3k36me3
#SBATCH --error=mergeandsort_h3k36me3
#SBATCH --partition=bigmem2
#SBATCH --mem=100G
#SBATCH --mail-type=END

source ~/activate_anaconda.sh
conda activate comp_threeprime_env

samtools merge ../data/H3K36me3/MergedIndiv.H3k36me3.bam  ../data/H3K36me3/*.bam

samtools sort ../data/H3K36me3/MergedIndiv.H3k36me3.bam  -o ../data/H3K36me3/MergedIndiv.H3k36me3.sort.bam 

samtools index ../data/H3K36me3/MergedIndiv.H3k36me3.sort.bam 
sbatch mergeandsorth3k36me3.sh 

bam to bigwig and dt plot


#!/bin/bash

#SBATCH --job-name=H3K36me3DTplot.sh
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=H3K36me3DTplot.out
#SBATCH --error=H3K36me3DTplot.err
#SBATCH --partition=bigmem2
#SBATCH --mem=100G
#SBATCH --mail-type=END


source ~/activate_anaconda.sh
conda activate comp_threeprime_env

bamCoverage -b ../data/H3K36me3/MergedIndiv.H3k36me3.sort.bam  -o ../data/H3K36me3/MergedIndiv.H3k36me3.sort.bw  

computeMatrix scale-regions -S ../data/H3K36me3/MergedIndiv.H3k36me3.sort.bw   -R ../data/PAS_doubleFilter/PAS_doublefilter_either_HumanCoordHummanUsage.sort.bed -b 500  -a 500 --skipZeros --transcript_id_designator 4 -out ../data/H3K36me3/H3k36me3PAS.gz

plotHeatmap --sortRegions descend -m ../data/H3K36me3/H3k36me3PAS.gz --plotTitle "PAS H3L36me3" --heatmapHeight 4 --colorMap magma  --averageTypeSummaryPlot "mean" --startLabel "5'"  --endLabel "3'" -out ../data/H3K36me3/H3k36me3PAS.png

H3K36me3DTplot.sh

Run this on distal 3’ UTRs PAS as well. I expect decrease after:

Look for most distal.

OverlapOrtho=read.table("../data/orthoUTR/FilteredPASOverlapOrthoUTR.text", header = T,stringsAsFactors = F) 

OverlapOrtho_plus= OverlapOrtho %>% filter(strand=="+") %>% group_by(geneUTR) %>% arrange(desc(endpas)) %>% slice(1)%>% ungroup() %>% select(PAS)

OverlapOrtho_neg= OverlapOrtho %>% filter(strand=="-") %>% group_by(geneUTR) %>% arrange(startpas) %>% slice(1) %>% ungroup() %>% select(PAS)

Overlapetiher= OverlapOrtho_plus %>% bind_rows(OverlapOrtho_neg)


#filter bed  

pasbed=read.table("../data/PAS_doubleFilter/PAS_doublefilter_either_HumanCoordHummanUsage.sort.bed", col.names = c("chr","start", "end", "PAS", "score", "strand"),stringsAsFactors = F) %>% inner_join(Overlapetiher,by="PAS")

write.table(pasbed, "../data/PAS_doubleFilter/DistalPAS_orthoUTR.bed", quote = F, col.names = F, row.names = F, sep="\t")

#!/bin/bash

#SBATCH --job-name=H3K36me3DTplot_distalPAS.sh
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=H3K36me3DTplot_distalPAS.out
#SBATCH --error=H3K36me3DTplot_distalPAS.err
#SBATCH --partition=bigmem2
#SBATCH --mem=100G
#SBATCH --mail-type=END


source ~/activate_anaconda.sh
conda activate comp_threeprime_env


computeMatrix scale-regions -S ../data/H3K36me3/MergedIndiv.H3k36me3.sort.bw   -R ../data/PAS_doubleFilter/DistalPAS_orthoUTR.bed -b 2000  -a 2000 --skipZeros --transcript_id_designator 4 -out ../data/H3K36me3/H3k36me3distalPAS.gz

plotHeatmap --sortRegions descend -m ../data/H3K36me3/H3k36me3distalPAS.gz --plotTitle "Distal UTR PAS H3L36me3" --heatmapHeight 4 --colorMap magma  --averageTypeSummaryPlot "mean" --startLabel "5'"  --endLabel "3'" -out ../data/H3K36me3/H3k36me3distalPAS.png


computeMatrix scale-regions -S ../data/H3K36me3/MergedIndiv.H3k36me3.sort.bw   -R ../data/PAS_doubleFilter/DistalPAS_orthoUTR.bed -b 10000  -a 10000 --skipZeros --transcript_id_designator 4 -out ../data/H3K36me3/H3k36me3distalPAS_longer.gz

plotHeatmap --sortRegions descend -m ../data/H3K36me3/H3k36me3distalPAS_longer.gz --plotTitle "Distal UTR PAS H3L36me3" --heatmapHeight 4 --colorMap magma  --averageTypeSummaryPlot "mean" --startLabel "5'"  --endLabel "3'" -out ../data/H3K36me3/H3k36me3distalPAS_longer.png

H3K36me3DTplot_distalPAS.sh

wider range for PAS


#!/bin/bash

#SBATCH --job-name=H3K36me3DTplotwide.sh
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=H3K36me3DTplotwide.out
#SBATCH --error=H3K36me3DTplotwide.err
#SBATCH --partition=bigmem2
#SBATCH --mem=100G
#SBATCH --mail-type=END


source ~/activate_anaconda.sh
conda activate comp_threeprime_env


computeMatrix scale-regions -S ../data/H3K36me3/MergedIndiv.H3k36me3.sort.bw   -R ../data/PAS_doubleFilter/PAS_doublefilter_either_HumanCoordHummanUsage.sort.bed -b 2000  -a 2000 --skipZeros --transcript_id_designator 4 -out ../data/H3K36me3/H3k36me3PASwide.gz

plotHeatmap --sortRegions descend -m ../data/H3K36me3/H3k36me3PASwide.gz --plotTitle "PAS H3L36me3" --heatmapHeight 4 --colorMap magma  --averageTypeSummaryPlot "mean" --startLabel "5'"  --endLabel "3'" -out ../data/H3K36me3/H3k36me3PASwide.png

Look at the level of h3k36me3 across full transcripts.

H3K36me3DTplot_transcript.sh

#!/bin/bash

#SBATCH --job-name=H3K36me3DTplot_transcript.sh
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=H3K36me3DTplot_transcript.out
#SBATCH --error=H3K36me3DTplot_transcript.err
#SBATCH --partition=broadwl
#SBATCH --mem=36G
#SBATCH --mail-type=END


source ~/activate_anaconda.sh
conda activate comp_threeprime_env


computeMatrix scale-regions -S ../data/H3K36me3/MergedIndiv.H3k36me3.sort.bw   -R /project2/gilad/briana/genome_anotation_data/hg38_refseq_anno/hg38_ncbiRefseq_transcripts.sort.bed -b 10000  -a 10000 --skipZeros --transcript_id_designator 4 -out ../data/H3K36me3/H3k36me3PASTranscript.gz

plotHeatmap --sortRegions descend -m ../data/H3K36me3/H3k36me3PASTranscript.gz --plotTitle "Transcript H3L36me3" --heatmapHeight 4 --colorMap magma  --averageTypeSummaryPlot "mean" --startLabel "TSS"  --endLabel "TES" -out ../data/H3K36me3/H3k36me3PASTranscript.png

Use H3K9me3 as a control:

H3K9me3

download

https://www.encodeproject.org/experiments/ENCSR000AOX/ (GM12878)

https://www.encodeproject.org/experiments/ENCSR673OPX/ ( GM23248)

H3K9me3_processandDT.sh

#!/bin/bash

#SBATCH --job-name=H3K9me3_processandDT
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=mergeandsort_H3K9me3
#SBATCH --error=mergeandsort_H3K9me3
#SBATCH --partition=bigmem2
#SBATCH --mem=100G
#SBATCH --mail-type=END

source ~/activate_anaconda.sh
conda activate comp_threeprime_env

samtools merge ../data/H3K36me3/MergedIndiv.H3K9me3.bam  ../data/H3K36me3/*H3K9me3.bam

samtools sort ../data/H3K36me3/MergedIndiv.H3K9me3.bam  -o ../data/H3K36me3/MergedIndiv.H3K9me3.sort.bam 

samtools index ../data/H3K36me3/MergedIndiv.H3K9me3.sort.bam 

bamCoverage -b ../data/H3K36me3/MergedIndiv.H3K9me3.sort.bam  -o ../data/H3K36me3/MergedIndiv.H3K9me3.sort.bw  


computeMatrix scale-regions -S ../data/H3K36me3/MergedIndiv.H3K9me3.sort.bw   -R ../data/PAS_doubleFilter/PAS_doublefilter_either_HumanCoordHummanUsage.sort.bed -b 500  -a 500 --skipZeros --transcript_id_designator 4 -out ../data/H3K36me3/H3K9me3PAS.gz

plotHeatmap --sortRegions descend -m ../data/H3K36me3/H3K9me3PAS.gz --plotTitle "PAS H3K9me3" --heatmapHeight 4 --colorMap magma  --averageTypeSummaryPlot "mean" --startLabel "5'"  --endLabel "3'" -out ../data/H3K36me3/H3K9me3PAS.png


computeMatrix scale-regions -S ../data/H3K36me3/MergedIndiv.H3K9me3.sort.bw   -R ../data/PAS_doubleFilter/PAS_doublefilter_either_HumanCoordHummanUsage.sort.bed -b 2000  -a 2000 --skipZeros --transcript_id_designator 4 -out ../data/H3K36me3/H3K9me3PASwide.gz

plotHeatmap --sortRegions descend -m ../data/H3K36me3/H3K9me3PASwide.gz --plotTitle "PAS H3K9me3" --heatmapHeight 4 --colorMap magma  --averageTypeSummaryPlot "mean" --startLabel "5'"  --endLabel "3'" -out ../data/H3K36me3/H3K9me3PASwide.png

computeMatrix scale-regions -S ../data/H3K36me3/MergedIndiv.H3K9me3.sort.bw   -R ../data/PAS_doubleFilter/DistalPAS_orthoUTR.bed -b 10000  -a 10000 --skipZeros --transcript_id_designator 4 -out ../data/H3K36me3/H3K9me3distalPAS_longer.gz

plotHeatmap --sortRegions descend -m ../data/H3K36me3/H3K9me3distalPAS_longer.gz --plotTitle "Distal UTR PAS H3K9me3" --heatmapHeight 4 --colorMap magma  --averageTypeSummaryPlot "mean" --startLabel "5'"  --endLabel "3'" -out ../data/H3K36me3/H3K9me3distalPAS_longer.png


computeMatrix scale-regions -S ../data/H3K36me3/MergedIndiv.H3K9me3.sort.bw   -R ../data/PAS_doubleFilter/PAS_doublefilter_either_HumanCoordHummanUsage.sort.bed -b 2000  -a 2000 --skipZeros --transcript_id_designator 4 -out ../data/H3K36me3/H3K9me3PASwide.gz

plotHeatmap --sortRegions descend -m ../data/H3K36me3/H3K9me3PASwide.gz --plotTitle "PAS H3K9me3" --heatmapHeight 4 --colorMap magma  --averageTypeSummaryPlot "mean" --startLabel "5'"  --endLabel "3'" -out ../data/H3K36me3/H3K9me3PASwide.png

H3K9me3DTplot_transcript.sh

#!/bin/bash

#SBATCH --job-name=H3K9me3DTplot_transcript.sh
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=H3K9me3DTplot_transcript.out
#SBATCH --error=H3K9me3DTplot_transcript.err
#SBATCH --partition=broadwl
#SBATCH --mem=36G
#SBATCH --mail-type=END


source ~/activate_anaconda.sh
conda activate comp_threeprime_env


computeMatrix scale-regions -S ../data/H3K36me3/MergedIndiv.H3K9me3.sort.bw   -R /project2/gilad/briana/genome_anotation_data/hg38_refseq_anno/hg38_ncbiRefseq_transcripts.sort.bed -b 10000  -a 10000 --skipZeros --transcript_id_designator 4 -out ../data/H3K36me3/H3K9me3PASTranscript.gz

plotHeatmap --sortRegions descend -m ../data/H3K36me3/H3K9me3PASTranscript.gz --plotTitle "Transcript H3K9me3" --heatmapHeight 4 --colorMap magma  --averageTypeSummaryPlot "mean" --startLabel "TSS"  --endLabel "TES" -out ../data/H3K36me3/H3K9me3PASTranscript.png

Conserved v non conserved

Now I can look at PAS by if they are differentially used and see if the signatures are different:

PASmeta=read.table("../data/PAS_doubleFilter/PAS_doublefilter_either_HumanCoordHummanUsage.sort.bed", col.names = c("chr","start", "end", "PAS", "score", "strand"),stringsAsFactors = F)
DiffIso=read.table("../data/DiffIso_Nuclear_DF/AllPAS_withGeneSig.txt",header = T,stringsAsFactors = F) %>% inner_join(PASmeta, by=c("chr", "start", "end"))

DiffIsoyes= DiffIso %>% filter(SigPAU2=="Yes") %>% select(PAS)
DiffIsono= DiffIso %>% filter(SigPAU2=="No") %>% select(PAS)


PASmeta_yes= PASmeta %>% inner_join(DiffIsoyes, by="PAS")
write.table(PASmeta_yes, "../data/PAS_doubleFilter/PAS_diffUsed.bed", quote = F, col.names = F, row.names = F, sep="\t")

PASmeta_no= PASmeta %>% inner_join(DiffIsono, by="PAS")
write.table(PASmeta_no, "../data/PAS_doubleFilter/PAS_NOTdiffUsed.bed", quote = F, col.names = F, row.names = F, sep="\t")

H3K36me3DTplot_DiffIso.sh

#!/bin/bash

#SBATCH --job-name=H3K36me3DTplot_DiffIso.sh
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=H3K36me3DTplot_DiffIso.out
#SBATCH --error=H3K36me3DTplot_DiffIso.err
#SBATCH --partition=bigmem2
#SBATCH --mem=64G
#SBATCH --mail-type=END


source ~/activate_anaconda.sh
conda activate comp_threeprime_env


computeMatrix scale-regions -S ../data/H3K36me3/MergedIndiv.H3k36me3.sort.bw -R ../data/PAS_doubleFilter/PAS_diffUsed.bed -b 1000  -a 1000 --skipZeros --transcript_id_designator 4 -out ../data/H3K36me3/H3k36me3PASDiffUsed.gz

plotHeatmap --sortRegions descend -m ../data/H3K36me3/H3k36me3PASDiffUsed.gz --plotTitle "Diff Used PAS H3K36me3" --heatmapHeight 4 --colorMap magma  --averageTypeSummaryPlot "mean" --startLabel "5'"  --endLabel "3'" -out ../data/H3K36me3/H3k36me3PASDiffUsed.png


computeMatrix scale-regions -S ../data/H3K36me3/MergedIndiv.H3k36me3.sort.bw  -R ../data/PAS_doubleFilter/PAS_NOTdiffUsed.bed -b 1000  -a 1000 --skipZeros --transcript_id_designator 4 -out ../data/H3K36me3/H3k36me3PASNOTDiffUsed.gz

plotHeatmap --sortRegions descend -m ../data/H3K36me3/H3k36me3PASNOTDiffUsed.gz --plotTitle "Conserved PAS H3K36me3" --heatmapHeight 4 --colorMap magma  --averageTypeSummaryPlot "mean" --startLabel "5'"  --endLabel "3'" -out ../data/H3K36me3/H3k36me3PASNOTDiffUsed.png

Human Specific, Chimp Specific

PAS=read.table("../data/PAS_doubleFilter/PAS_5perc_either_HumanCoord_BothUsage_meta_doubleFilter.txt", header = T, stringsAsFactors = F)

HumanSpec= PAS %>% filter(Chimp==0)
ChimpSpec= PAS %>% filter(Human==0)
PASmetaHS= PASmeta %>% filter(PAS %in% HumanSpec$PAS)
PASmetaCS= PASmeta %>% filter(PAS %in% ChimpSpec$PAS)

write.table(PASmetaHS, "../data/PAS_doubleFilter/PAS_HumanSpecifc.bed", quote = F, col.names = F, row.names = F, sep="\t")

write.table(PASmetaCS, "../data/PAS_doubleFilter/PAS_ChimpSpecifc.bed", quote = F, col.names = F, row.names = F, sep="\t")

H3K36me3DTplot_Specific.sh

#!/bin/bash

#SBATCH --job-name=H3K36me3DTplot_Specific.sh
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=H3K36me3DTplot_Specific.out
#SBATCH --error=H3K36me3DTplot_Specific.err
#SBATCH --partition=bigmem2
#SBATCH --mem=64G
#SBATCH --mail-type=END


source ~/activate_anaconda.sh
conda activate comp_threeprime_env


computeMatrix scale-regions -S ../data/H3K36me3/MergedIndiv.H3k36me3.sort.bw -R ../data/PAS_doubleFilter/PAS_HumanSpecifc.bed -b 1000  -a 1000 --skipZeros --transcript_id_designator 4 -out ../data/H3K36me3/H3k36me3HumanSpec.gz

plotHeatmap --sortRegions descend -m ../data/H3K36me3/H3k36me3HumanSpec.gz --plotTitle "Human Specific H3K36me3" --heatmapHeight 4 --colorMap magma  --averageTypeSummaryPlot "mean" --startLabel "5'"  --endLabel "3'" -out ../data/H3K36me3/H3k36me3HumanSpec.png


computeMatrix scale-regions -S ../data/H3K36me3/MergedIndiv.H3k36me3.sort.bw  -R ../data/PAS_doubleFilter/PAS_ChimpSpecifc.bed -b 1000  -a 1000 --skipZeros --transcript_id_designator 4 -out ../data/H3K36me3/H3k36me3ChimpSpec.gz

plotHeatmap --sortRegions descend -m ../data/H3K36me3/H3k36me3ChimpSpec.gz --plotTitle "Chimp Specific H3K36me3" --heatmapHeight 4 --colorMap magma  --averageTypeSummaryPlot "mean" --startLabel "5'"  --endLabel "3'" -out ../data/H3K36me3/H3k36me3ChimpSpec.png

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] forcats_0.3.0   stringr_1.3.1   dplyr_0.8.0.1   purrr_0.3.2    
[5] readr_1.3.1     tidyr_0.8.3     tibble_2.1.1    ggplot2_3.1.1  
[9] tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6     cellranger_1.1.0 plyr_1.8.4       compiler_3.5.1  
 [5] pillar_1.3.1     later_0.7.5      git2r_0.26.1     workflowr_1.6.0 
 [9] tools_3.5.1      digest_0.6.18    lubridate_1.7.4  jsonlite_1.6    
[13] evaluate_0.12    nlme_3.1-137     gtable_0.2.0     lattice_0.20-38 
[17] pkgconfig_2.0.2  rlang_0.4.0      cli_1.1.0        rstudioapi_0.10 
[21] yaml_2.2.0       haven_1.1.2      withr_2.1.2      xml2_1.2.0      
[25] httr_1.3.1       knitr_1.20       hms_0.4.2        generics_0.0.2  
[29] fs_1.3.1         rprojroot_1.3-2  grid_3.5.1       tidyselect_0.2.5
[33] glue_1.3.0       R6_2.3.0         readxl_1.1.0     rmarkdown_1.10  
[37] modelr_0.1.2     magrittr_1.5     whisker_0.3-2    backports_1.1.2 
[41] scales_1.0.0     promises_1.0.1   htmltools_0.3.6  rvest_0.3.2     
[45] assertthat_0.2.0 colorspace_1.3-2 httpuv_1.4.5     stringi_1.2.4   
[49] lazyeval_0.2.1   munsell_0.5.0    broom_0.5.1      crayon_1.3.4