Last updated: 2020-02-18

Checks: 6 1

Knit directory: apaQTL/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.

R Markdown file: up-to-date

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.

Environment: empty

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.

Seed: set.seed(20190411)

The command set.seed(20190411) 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.

Session information: recorded

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

Cache: none

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

File paths: absolute

Using absolute paths to the files within your workflowr project makes it difficult for you and others to run your code on a different machine. Change the absolute path(s) below to the suggested relative path(s) to make your code more reproducible.

absolute relative
/project2/gilad/briana/apaQTL/data/intron_analysis/transcriptsMinusExons.sort.bed ../data/intron_analysis/transcriptsMinusExons.sort.bed

Repository version: fe3acb2

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:    data/.DS_Store
    Ignored:    data/ProSeq/
    Ignored:    output/.DS_Store

Untracked files:
    Untracked:  .Rprofile
    Untracked:  ._.DS_Store
    Untracked:  .gitignore
    Untracked:  @
    Untracked:  GEO_brimittleman/
    Untracked:  _workflowr.yml
    Untracked:  analysis/._PASdescriptiveplots.Rmd
    Untracked:  analysis/._cuttoffPercUsage.Rmd
    Untracked:  analysis/APApeak_Phenotype_GeneLocAnno.Nuclear.5perc.fc.gz.qqnorm.allChrom
    Untracked:  analysis/APApeak_Phenotype_GeneLocAnno.Total.5perc.fc.gz.qqnorm.allChrom
    Untracked:  analysis/QTLexampleplots.Rmd
    Untracked:  analysis/cuttoffPercUsage.Rmd
    Untracked:  analysis/eQTLoverlap.Rmd
    Untracked:  analysis/interpret verify bam.Rmd
    Untracked:  analysis/interpret_verifybam.Rmd
    Untracked:  analysis/mergeRNA.Rmd
    Untracked:  analysis/oldstuffNotNeeded.Rmd
    Untracked:  analysis/remove_badlines.Rmd
    Untracked:  analysis/totSpecInNuclear.Rmd
    Untracked:  analysis/totSpecIncludenotTested.Rmd
    Untracked:  analysis/totalspec.Rmd
    Untracked:  apaQTL.Rproj
    Untracked:  checksumsfastq.txt.gz
    Untracked:  code/.NascentRNAdtPlotFirstintronicPAS.sh.swp
    Untracked:  code/._ApaQTL_nominalNonnorm.sh
    Untracked:  code/._BothFracDTPlotGeneRegions.sh
    Untracked:  code/._BothFracDTPlotGeneRegions_normalized.sh
    Untracked:  code/._ClosestTissuePAS.sh
    Untracked:  code/._CreateRNALZforeQTLs.sh
    Untracked:  code/._CreateRNALZnucAPAqtls.sh
    Untracked:  code/._DistPAS2Sig_RandomIntron.py
    Untracked:  code/._EandPqtl_perm.sh
    Untracked:  code/._EandPqtls.sh
    Untracked:  code/._ExtractGene4eQTLLZ.py
    Untracked:  code/._ExtractGene4eQTLLZpy
    Untracked:  code/._ExtractGeneRNAAssoc.py
    Untracked:  code/._ExtractPAS4LZeQTLs.py
    Untracked:  code/._ExtractPAS4eQTLsLZ.sh
    Untracked:  code/._ExtractPASforLZ.py
    Untracked:  code/._ExtractPASforLZ_run.sh
    Untracked:  code/._FC_NucintornUpandDown.sh
    Untracked:  code/._FC_UTR.sh
    Untracked:  code/._FC_intornUpandDownsteamPAS.sh
    Untracked:  code/._FC_nascentseq.sh
    Untracked:  code/._FC_newPeaks_olddata.sh
    Untracked:  code/._HMMpermuteTotal.py
    Untracked:  code/._HmmPermute.py
    Untracked:  code/._IntronicPASDT.sh
    Untracked:  code/._LC_samplegroups.py
    Untracked:  code/._LD_qtl.sh
    Untracked:  code/._LD_snpsproxy.sh
    Untracked:  code/._MapAllRBP.sh
    Untracked:  code/._NascentRNAdtPlot.sh
    Untracked:  code/._NascentRNAdtPlot3UTRPAS.sh
    Untracked:  code/._NascentRNAdtPlotExcludeFirstintronicPAS.sh
    Untracked:  code/._NascentRNAdtPlotNucPAS.sh
    Untracked:  code/._NascentRNAdtPlotTotPAS.sh
    Untracked:  code/._NascentRNAdtPlotintronicPAS.sh
    Untracked:  code/._NascnetRNAdtPlotPAS.sh
    Untracked:  code/._NetSeq_fourthintronDT.sh
    Untracked:  code/._NomResfromPASSNP.py
    Untracked:  code/._NuclearPAS_5per.bed.py
    Untracked:  code/._NuclearandRNA5samp_dtplots.sh
    Untracked:  code/._PTTfacetboxplots.R
    Untracked:  code/._PrematureQTLNominal.sh
    Untracked:  code/._PrematureQTLPermuted.sh
    Untracked:  code/._QTL2bed.py
    Untracked:  code/._QTL2bed_withstrand.py
    Untracked:  code/._RBPdisrupt.sh
    Untracked:  code/._RNAbam2bw.sh
    Untracked:  code/._RNAseqDTplot.sh
    Untracked:  code/._Randomsplicesite2fasta.py
    Untracked:  code/._Rplots.pdf
    Untracked:  code/._RunRes2PAS.sh
    Untracked:  code/._SAF215upbed.py
    Untracked:  code/._SnakefilePAS
    Untracked:  code/._SnakefilefiltPAS
    Untracked:  code/._TESplots100bp.sh
    Untracked:  code/._TESplots150bp.sh
    Untracked:  code/._TESplots200bp.sh
    Untracked:  code/._TotalPAS_5perc.bed.py
    Untracked:  code/._Untitled
    Untracked:  code/._ZipandTabPheno.sh
    Untracked:  code/._aAPAqtl_nominal39ind.sh
    Untracked:  code/._allNucSpecQTLine.py
    Untracked:  code/._allNucSpecfromNonNorm.py
    Untracked:  code/._annotatePacBioPASregion.sh
    Untracked:  code/._annotatedPAS2bed.py
    Untracked:  code/._apaInPandE.py
    Untracked:  code/._apaQTLCorrectPvalMakeQQ.R
    Untracked:  code/._apaQTLCorrectpval_6or7a.R
    Untracked:  code/._apaQTL_Nominal.sh
    Untracked:  code/._apaQTL_nominalInclusive.sh
    Untracked:  code/._apaQTL_nominalv67.sh
    Untracked:  code/._apaQTL_permuted.sh
    Untracked:  code/._apaQTL_permuted_test6A7A.sh
    Untracked:  code/._apainRibo.py
    Untracked:  code/._assignNucIntonpeak2intronlocs.sh
    Untracked:  code/._assignTotIntronpeak2intronlocs.sh
    Untracked:  code/._bam2BW_5primemost.sh
    Untracked:  code/._bed2saf.py
    Untracked:  code/._bothFracDTplot1stintron.sh
    Untracked:  code/._bothFracDTplot4thintron.sh
    Untracked:  code/._bothFrac_FC.sh
    Untracked:  code/._callPeaksYL.py
    Untracked:  code/._changeRibonomQTLres2genename.py
    Untracked:  code/._changenomQTLres2geneName.py
    Untracked:  code/._chooseAnno2PAS_pacbio.py
    Untracked:  code/._chooseAnno2SAF.py
    Untracked:  code/._chooseSignalSite
    Untracked:  code/._chooseSignalSite.py
    Untracked:  code/._closestannotated.sh
    Untracked:  code/._closestannotated_byfrac.sh
    Untracked:  code/._cluster.json
    Untracked:  code/._clusterPAS.json
    Untracked:  code/._clusterfiltPAS.json
    Untracked:  code/._codingdms2bed.py
    Untracked:  code/._config.yaml
    Untracked:  code/._config2.yaml
    Untracked:  code/._configOLD.yaml
    Untracked:  code/._convertNominal2SNPLOC.py
    Untracked:  code/._convertNominal2SNPloc2Versions.py
    Untracked:  code/._convertNumeric.py
    Untracked:  code/._correctNomeqtl.R
    Untracked:  code/._createPlinkSampfile.py
    Untracked:  code/._dag.pdf
    Untracked:  code/._eQTL_switch2snploc.py
    Untracked:  code/._eQTLgenestestedapa.py
    Untracked:  code/._encodeRNADTplots.sh
    Untracked:  code/._extactPAS100meanphyloP.py
    Untracked:  code/._extractGeneLZfiles.sh
    Untracked:  code/._extractGeneLZfileseQTLs.sh
    Untracked:  code/._extractGenotypes.py
    Untracked:  code/._extractPACmeanPhyloP.py
    Untracked:  code/._extractPhylop50up.py
    Untracked:  code/._extractPhylopextra50.py
    Untracked:  code/._extractRNApval4lz.py
    Untracked:  code/._extractseqfromqtlfastq.py
    Untracked:  code/._fc2leafphen.py
    Untracked:  code/._fc_filteredPAS6and7As.sh
    Untracked:  code/._fifteenBPupstreamPAS.py
    Untracked:  code/._fiftyBPupstreamPAS.py
    Untracked:  code/._filter5perc.R
    Untracked:  code/._filter5percPheno.py
    Untracked:  code/._filterLDsnps.py
    Untracked:  code/._filterMPPAS.py
    Untracked:  code/._filterMPPAS_15.py
    Untracked:  code/._filterMPPAS_15_7As.py
    Untracked:  code/._filterMPPAS_50.py
    Untracked:  code/._filterSAFforMP.py
    Untracked:  code/._filterpeaks.py
    Untracked:  code/._finalPASbed2SAF.py
    Untracked:  code/._fix4su304corr.py
    Untracked:  code/._fix4su604corr.py
    Untracked:  code/._fix4sukalisto.py
    Untracked:  code/._fixExandUnexeQTL
    Untracked:  code/._fixExandUnexeQTL.py
    Untracked:  code/._fixFChead.py
    Untracked:  code/._fixFChead_bothfrac.py
    Untracked:  code/._fixFChead_short.py
    Untracked:  code/._fixGWAS4Munge.py
    Untracked:  code/._fixH3k12ac.py
    Untracked:  code/._fixPASregionSNPs.py
    Untracked:  code/._fixRNAhead4corr.py
    Untracked:  code/._fixRNAkalisto.py
    Untracked:  code/._fix_randomIntron.py
    Untracked:  code/._fixgroupedtranscript.py
    Untracked:  code/._fixhead_netseqfc.py
    Untracked:  code/._getAPAfromanyeQTL.py
    Untracked:  code/._getApapval4eqtl.py
    Untracked:  code/._getApapval4eqtl_unexp.py
    Untracked:  code/._getApapval4eqtl_version67.py
    Untracked:  code/._getDownstreamIntronNuclear.py
    Untracked:  code/._getIntronDownstreamPAS.py
    Untracked:  code/._getIntronUpstreamPAS.py
    Untracked:  code/._getQTLalleles.py
    Untracked:  code/._getQTLfastq.sh
    Untracked:  code/._getUpstreamIntronNuclear.py
    Untracked:  code/._grouptranscripts.py
    Untracked:  code/._intersectVCFandupPAS.sh
    Untracked:  code/._keep5perMAF.py
    Untracked:  code/._keepSNP_vcf.sh
    Untracked:  code/._make5percPeakbed.py
    Untracked:  code/._makeFileID.py
    Untracked:  code/._makePheno.py
    Untracked:  code/._makeSAFbothfrac5perc.py
    Untracked:  code/._makeSNP2rsidfile.py
    Untracked:  code/._makeeQTLempirical_unexp.py
    Untracked:  code/._makeeQTLempiricaldist.py
    Untracked:  code/._makegencondeTSSfile.py
    Untracked:  code/._mapSSsnps2PAS.sh
    Untracked:  code/._mergRNABam.sh
    Untracked:  code/._mergeAllBam.sh
    Untracked:  code/._mergeAnnotations.sh
    Untracked:  code/._mergeBW_norm.sh
    Untracked:  code/._mergeBamNascent.sh
    Untracked:  code/._mergeByFracBam.sh
    Untracked:  code/._mergePeaks.sh
    Untracked:  code/._miRNAdisrupt.sh
    Untracked:  code/._mnase1stintron.sh
    Untracked:  code/._mnaseDT_fourthintron.sh
    Untracked:  code/._namePeaks.py
    Untracked:  code/._netseqDTplot1stIntron.sh
    Untracked:  code/._netseqFC.sh
    Untracked:  code/._nucQTLGWAS.py
    Untracked:  code/._nucSpecQTLineData.py
    Untracked:  code/._nucSpeceffectsize.py
    Untracked:  code/._nucspecnucPASine.py
    Untracked:  code/._pQTLsotherdata.py
    Untracked:  code/._pacbioDT.sh
    Untracked:  code/._pacbioIntronicDT.sh
    Untracked:  code/._parseBestbamid.py
    Untracked:  code/._parseLDRes.py
    Untracked:  code/._parseLDresBothPAS.sh
    Untracked:  code/._parseRanodmSSres.py
    Untracked:  code/._parseSSres.py
    Untracked:  code/._peak2PAS.py
    Untracked:  code/._peakFC.sh
    Untracked:  code/._pheno2countonly.R
    Untracked:  code/._phenoQTLfromlist.py
    Untracked:  code/._processYRIgen.py
    Untracked:  code/._pttQTLsinapaQTL.py
    Untracked:  code/._qtlRegionseq.sh
    Untracked:  code/._qtlsPvalOppFrac.py
    Untracked:  code/._quantassign2parsedpeak.py
    Untracked:  code/._removeXfromHmm.py
    Untracked:  code/._removeloc_pheno.py
    Untracked:  code/._riboQTL.sh
    Untracked:  code/._runCorrectNomEqtl.sh
    Untracked:  code/._runFixGWAS4Munge.sh
    Untracked:  code/._runHMMpermuteAPAqtls.sh
    Untracked:  code/._runHMMpermuteeQTLS.sh
    Untracked:  code/._runMakeEmpiricaleQTL_unexp.sh
    Untracked:  code/._runMakeeQTLempirical.sh
    Untracked:  code/._run_bam2bw_all3prime.sh
    Untracked:  code/._run_bam2bw_extra3.sh
    Untracked:  code/._run_bestbamid.sj
    Untracked:  code/._run_dist2sig_randomintron.sh
    Untracked:  code/._run_filtersnpLD.sh
    Untracked:  code/._run_getAPAfromeQTL_version6.7.sh
    Untracked:  code/._run_getApaPval4eqtl.sh
    Untracked:  code/._run_getapafromeQTL.py
    Untracked:  code/._run_getapafromeQTL.sh
    Untracked:  code/._run_getapapval4eqtl_unexp.sh
    Untracked:  code/._run_leafcutterDiffIso.sh
    Untracked:  code/._run_prxySNP.sh
    Untracked:  code/._run_pttfacetboxplot.sh
    Untracked:  code/._run_sepUsagephen.sh
    Untracked:  code/._run_sepgenobychrom.sh
    Untracked:  code/._run_verifybam.sh
    Untracked:  code/._selectNominalPvalues.py
    Untracked:  code/._sepUsagePhen.py
    Untracked:  code/._sepgenobychrom.py
    Untracked:  code/._snakemakePAS.batch
    Untracked:  code/._snakemakefiltPAS.batch
    Untracked:  code/._sortindexRNAbam.sh
    Untracked:  code/._specAPAinE.py
    Untracked:  code/._splicesite2fasta.py
    Untracked:  code/._submit-snakemakePAS.sh
    Untracked:  code/._submit-snakemakefiltPAS.sh
    Untracked:  code/._subsetAPAnotEorPgene.py
    Untracked:  code/._subsetAPAnotEorPgene_2versions.py
    Untracked:  code/._subsetApanoteGene.py
    Untracked:  code/._subsetApanoteGene_2versions.py
    Untracked:  code/._subsetUnexplainedeQTLs.py
    Untracked:  code/._subsetVCF_SS.sh
    Untracked:  code/._subsetVCF_noSSregions.sh
    Untracked:  code/._subsetVCF_upstreamPAS.sh
    Untracked:  code/._subset_diffisopheno.py
    Untracked:  code/._subsetpermAPAwithGenelist.py
    Untracked:  code/._subsetpermAPAwithGenelist_2versions.py
    Untracked:  code/._subsetvcf_otherreg.sh
    Untracked:  code/._subsetvcf_permSS.sh
    Untracked:  code/._subtrachfiveprimeUTR.sh
    Untracked:  code/._subtractExons.sh
    Untracked:  code/._subtractfiveprimeUTR.sh
    Untracked:  code/._tabixSNPS.sh
    Untracked:  code/._tenBPupstreamPAS.py
    Untracked:  code/._test.pdf
    Untracked:  code/._testVerifyBam.sh
    Untracked:  code/._tissuePAS2hg19.sh
    Untracked:  code/._totSeceffectsize.py
    Untracked:  code/._twentyBPupstreamPAS.py
    Untracked:  code/._utrdms2saf.py
    Untracked:  code/._vcf2bed.py
    Untracked:  code/._verifyBam18517N.sh
    Untracked:  code/._verifyBam18517T.sh
    Untracked:  code/._verifyBam19128N.sh
    Untracked:  code/._verifyBam19128T.sh
    Untracked:  code/._wrap_verifybam.sh
    Untracked:  code/._writePTTexamplecode.py
    Untracked:  code/._writePTTexamplecode.sh
    Untracked:  code/.pversion
    Untracked:  code/.snakemake/
    Untracked:  code/1
    Untracked:  code/APAqtl_nominal.err
    Untracked:  code/APAqtl_nominal.out
    Untracked:  code/APAqtl_nominal_39.err
    Untracked:  code/APAqtl_nominal_39.out
    Untracked:  code/APAqtl_nominal_inclusive.err
    Untracked:  code/APAqtl_nominal_inclusive.out
    Untracked:  code/APAqtl_nominal_nonNorm.err
    Untracked:  code/APAqtl_nominal_nonNorm.out
    Untracked:  code/APAqtl_nominal_versions67.err
    Untracked:  code/APAqtl_nominal_versions67.out
    Untracked:  code/APAqtl_permuted.err
    Untracked:  code/APAqtl_permuted.out
    Untracked:  code/APAqtl_permuted_versions67.err
    Untracked:  code/APAqtl_permuted_versions67.out
    Untracked:  code/BothFracDTPlot1stintron.err
    Untracked:  code/BothFracDTPlot1stintron.out
    Untracked:  code/BothFracDTPlot4stintron.err
    Untracked:  code/BothFracDTPlot4stintron.out
    Untracked:  code/BothFracDTPlotGeneRegions.err
    Untracked:  code/BothFracDTPlotGeneRegions.out
    Untracked:  code/BothFracDTPlotGeneRegions_norm.err
    Untracked:  code/BothFracDTPlotGeneRegions_norm.out
    Untracked:  code/ClosestTissuePAS.sh
    Untracked:  code/CreateRNALZforeQTLs.sh
    Untracked:  code/CreateRNALZnucAPAqtls.sh
    Untracked:  code/DistPAS2Sig_RandomIntron.py
    Untracked:  code/EandPqtl.err
    Untracked:  code/EandPqtl.out
    Untracked:  code/EncodeRNADTPlotGeneRegions.err
    Untracked:  code/EncodeRNADTPlotGeneRegions.out
    Untracked:  code/ExtractGene4eQTLLZ.py
    Untracked:  code/ExtractGene4eQTLLZpy
    Untracked:  code/ExtractGeneRNAAssoc.py
    Untracked:  code/ExtractPAS4LZeQTLs.py
    Untracked:  code/ExtractPAS4eQTLsLZ.sh
    Untracked:  code/ExtractPASforLZ.py
    Untracked:  code/ExtractPASforLZ_run.sh
    Untracked:  code/FC_NucintronPASupandDown.err
    Untracked:  code/FC_NucintronPASupandDown.out
    Untracked:  code/FC_UTR.err
    Untracked:  code/FC_UTR.out
    Untracked:  code/FC_intronPASupandDown.err
    Untracked:  code/FC_intronPASupandDown.out
    Untracked:  code/FC_nascent.err
    Untracked:  code/FC_nascentout
    Untracked:  code/FC_newPAS_olddata.err
    Untracked:  code/FC_newPAS_olddata.out
    Untracked:  code/HmmPermute.p
    Untracked:  code/IntronicPASDT.err
    Untracked:  code/IntronicPASDT.out
    Untracked:  code/LD_vcftools.hap.out
    Untracked:  code/MapAllRBP.sh
    Untracked:  code/MapRBP.err
    Untracked:  code/MapRBP.out
    Untracked:  code/NascentDTPlotGeneRegions.err
    Untracked:  code/NascentDTPlotGeneRegions.out
    Untracked:  code/NascentDTPlotPAS.err
    Untracked:  code/NascentDTPlotPAS.out
    Untracked:  code/NascentDTPlotPAS_3utr.err
    Untracked:  code/NascentDTPlotPAS_3utr.out
    Untracked:  code/NascentDTPlotPAS_firstintron.err
    Untracked:  code/NascentDTPlotPAS_firstintron.out
    Untracked:  code/NascentDTPlotPAS_intron.err
    Untracked:  code/NascentDTPlotPAS_intron.out
    Untracked:  code/NascentDTPlotPAS_nuc.err
    Untracked:  code/NascentDTPlotPAS_nuc.out
    Untracked:  code/NascentDTPlotPAS_tot.err
    Untracked:  code/NascentDTPlotPAS_tot.out
    Untracked:  code/Nuclear_example.err
    Untracked:  code/Nuclear_example.out
    Untracked:  code/NuclearandRNA5samp_dtplots.sh
    Untracked:  code/NuclearandRNAFracDTPlotGeneRegions.err
    Untracked:  code/NuclearandRNAFracDTPlotGeneRegions.out
    Untracked:  code/PACbioDT.err
    Untracked:  code/PACbioDT.out
    Untracked:  code/PACbioDTitronic.err
    Untracked:  code/PACbioDTitronic.out
    Untracked:  code/Prematureqtl_nominal.err
    Untracked:  code/Prematureqtl_nominal.out
    Untracked:  code/Prematureqtl_permuted.err
    Untracked:  code/Prematureqtl_permuted.out
    Untracked:  code/RBPdisrupt.err
    Untracked:  code/RBPdisrupt.out
    Untracked:  code/RBPdisrupt.sh
    Untracked:  code/README.md
    Untracked:  code/RNABam2BW.err
    Untracked:  code/RNABam2BW.out
    Untracked:  code/RNAseqDTPlotGeneRegions.err
    Untracked:  code/RNAseqDTPlotGeneRegions.out
    Untracked:  code/Randomsplicesite2fasta.py
    Untracked:  code/Rplots.pdf
    Untracked:  code/TESplots100bp.err
    Untracked:  code/TESplots100bp.out
    Untracked:  code/TESplots150bp.err
    Untracked:  code/TESplots150bp.out
    Untracked:  code/TESplots200bp.err
    Untracked:  code/TESplots200bp.out
    Untracked:  code/Tissueclosestannotated.err
    Untracked:  code/Tissueclosestannotated.out
    Untracked:  code/Total_example.err
    Untracked:  code/Total_example.out
    Untracked:  code/Untitled
    Untracked:  code/YRI_LCL.vcf.gz
    Untracked:  code/YRI_LCL_chr1.vcf.gz.log
    Untracked:  code/YRI_LCL_chr1.vcf.gz.recode.vcf
    Untracked:  code/annotatedPASregion.err
    Untracked:  code/annotatedPASregion.out
    Untracked:  code/apaQTL_nominalInclusive.sh
    Untracked:  code/assignPeak2Intronicregion.err
    Untracked:  code/assignPeak2Intronicregion.out
    Untracked:  code/assigntotPeak2Intronicregion.err
    Untracked:  code/assigntotPeak2Intronicregion.out
    Untracked:  code/bam2bw.err
    Untracked:  code/bam2bw.out
    Untracked:  code/bam2bw_5primemost.err
    Untracked:  code/bam2bw_5primemost.out
    Untracked:  code/binary_fileset.log
    Untracked:  code/bothFrac_FC.err
    Untracked:  code/bothFrac_FC.out
    Untracked:  code/callSHscripts.txt
    Untracked:  code/closestannotated.err
    Untracked:  code/closestannotated.out
    Untracked:  code/closestannotatedbyfrac.err
    Untracked:  code/closestannotatedbyfrac.out
    Untracked:  code/dag.pdf
    Untracked:  code/dagPAS.pdf
    Untracked:  code/dagfiltPAS.pdf
    Untracked:  code/extactPAS100meanphyloP.py
    Untracked:  code/extractGeneLZfiles.err
    Untracked:  code/extractGeneLZfiles.out
    Untracked:  code/extractGeneLZfiles.sh
    Untracked:  code/extractGeneLZfileseQTLs.err
    Untracked:  code/extractGeneLZfileseQTLs.out
    Untracked:  code/extractGeneLZfileseQTLs.sh
    Untracked:  code/extractPACmeanPhyloP.py
    Untracked:  code/extractPASLZfiles.err
    Untracked:  code/extractPASLZfiles.out
    Untracked:  code/extractPASLZfileseQTLs.err
    Untracked:  code/extractPASLZfileseQTLs.out
    Untracked:  code/extractPhylop50up.py
    Untracked:  code/extractPhylopextra50.py
    Untracked:  code/extractRNApval4lz.py
    Untracked:  code/fixExandUnexeQTL
    Untracked:  code/fixGWAS4Munge.py
    Untracked:  code/fix_randomIntron.py
    Untracked:  code/fixmunge
    Untracked:  code/genotypesYRI.gen.proc.keep.vcf.log
    Untracked:  code/genotypesYRI.gen.proc.keep.vcf.recode.vcf
    Untracked:  code/getseq100up.err
    Untracked:  code/getseq100up.out
    Untracked:  code/grouptranscripts.err
    Untracked:  code/grouptranscripts.out
    Untracked:  code/intersectPAS_ssSNPS.err
    Untracked:  code/intersectPAS_ssSNPS.out
    Untracked:  code/intersectVCFPAS.err
    Untracked:  code/intersectVCFPAS.out
    Untracked:  code/liftoverPAShg38to19.err
    Untracked:  code/liftoverPAShg38to19.out
    Untracked:  code/log/
    Untracked:  code/logs/
    Untracked:  code/merge53PRIMEbam.err
    Untracked:  code/merge53PRIMEbam.out
    Untracked:  code/merge53RNAbam.err
    Untracked:  code/merge53prime.sh
    Untracked:  code/merge5RNABam.err
    Untracked:  code/merge5RNABam.out
    Untracked:  code/merge5RNAbam.out
    Untracked:  code/merge5RNAbam.sh
    Untracked:  code/mergeAnno.err
    Untracked:  code/mergeAnno.out
    Untracked:  code/mergeBWnorm.err
    Untracked:  code/mergeBWnorm.out
    Untracked:  code/mergeBamNacent.err
    Untracked:  code/mergeBamNacent.out
    Untracked:  code/mergeRNAbam.err
    Untracked:  code/mergeRNAbam.out
    Untracked:  code/miRNAdisrupt.err
    Untracked:  code/miRNAdisrupt.out
    Untracked:  code/miRNAdisrupt.sh
    Untracked:  code/mnaseDTPlot1stintron.err
    Untracked:  code/mnaseDTPlot1stintron.out
    Untracked:  code/mnaseDTPlot4thintron.err
    Untracked:  code/mnaseDTPlot4thintron.out
    Untracked:  code/netDTPlot4thintron.out
    Untracked:  code/netseqFC.err
    Untracked:  code/netseqFC.out
    Untracked:  code/neyDTPlot4thintron.err
    Untracked:  code/nucspecinE.py
    Untracked:  code/parseLDRes.py
    Untracked:  code/parseLDres.err
    Untracked:  code/parseLDres.out
    Untracked:  code/parseLDresBothPAS.sh
    Untracked:  code/parseRanodmSSres.py
    Untracked:  code/parseSSres.py
    Untracked:  code/plink.log
    Untracked:  code/prxySNP.err
    Untracked:  code/prxySNP.out
    Untracked:  code/pttFacetBoxplots.err
    Untracked:  code/pttFacetBoxplots.out
    Untracked:  code/qtlFacetBoxplots.err
    Untracked:  code/qtlFacetBoxplots.out
    Untracked:  code/rLD_vcftools.hap.err
    Untracked:  code/riboqtl.err
    Untracked:  code/riboqtl.out
    Untracked:  code/runBestBamID.err
    Untracked:  code/runCorrectNomeqtl.err
    Untracked:  code/runCorrectNomeqtl.out
    Untracked:  code/runFilterLD.err
    Untracked:  code/runFilterLD.out
    Untracked:  code/runFixGWAS4Munge.sh
    Untracked:  code/runHMMpermute.err
    Untracked:  code/runHMMpermute.out
    Untracked:  code/runHMMpermuteeQTLs.err
    Untracked:  code/runHMMpermuteeQTLs.out
    Untracked:  code/runMakeEmpiricaleQTLs.err
    Untracked:  code/runMakeEmpiricaleQTLs.out
    Untracked:  code/runMakeEmpiricaleQTLsunex.err
    Untracked:  code/runMakeEmpiricaleQTLsunex.out
    Untracked:  code/run_DistPAS2Sig.err
    Untracked:  code/run_DistPAS2Sig.out
    Untracked:  code/run_DistPAS2Sig_intron.err
    Untracked:  code/run_DistPAS2Sig_intron.out
    Untracked:  code/run_bam2bw.err
    Untracked:  code/run_bam2bw.out
    Untracked:  code/run_bam2bwexta.err
    Untracked:  code/run_bam2bwexta.out
    Untracked:  code/run_dist2sig_randomintron.sh
    Untracked:  code/run_getAPAfromanyeQTL.err
    Untracked:  code/run_getAPAfromanyeQTL.out
    Untracked:  code/run_getApaPval4eQTLs.err
    Untracked:  code/run_getApaPval4eQTLs.out
    Untracked:  code/run_getApaPval4eQTLsunexplained.err
    Untracked:  code/run_getApaPval4eQTLsunexplained.out
    Untracked:  code/run_leafcutter_ds.err
    Untracked:  code/run_leafcutter_ds.out
    Untracked:  code/run_sepgenobychrom.err
    Untracked:  code/run_sepgenobychrom.out
    Untracked:  code/run_sepusage.err
    Untracked:  code/run_sepusage.out
    Untracked:  code/run_verifybam.err
    Untracked:  code/run_verifybam.out
    Untracked:  code/run_verifybam128N.err
    Untracked:  code/run_verifybam128N.out
    Untracked:  code/run_verifybam128T.err
    Untracked:  code/run_verifybam128T.out
    Untracked:  code/run_verifybam517N.err
    Untracked:  code/run_verifybam517N.out
    Untracked:  code/run_verifybam517T.err
    Untracked:  code/run_verifybam517T.out
    Untracked:  code/runprxySNP.err
    Untracked:  code/runprxySNP.out
    Untracked:  code/runres2pas.err
    Untracked:  code/runres2pas.out
    Untracked:  code/scripts/
    Untracked:  code/scripts_PAS_500_Lymph/
    Untracked:  code/seqQTLfastq.err
    Untracked:  code/seqQTLfastq.out
    Untracked:  code/seqQTLregion.err
    Untracked:  code/seqQTLregion.out
    Untracked:  code/snakePASlog.out
    Untracked:  code/snakefiltPASlog.out
    Untracked:  code/sortindexRNABam.err
    Untracked:  code/sortindexRNABam.out
    Untracked:  code/specAPAinE.py
    Untracked:  code/splicesite2fasta.py
    Untracked:  code/subsetvcf_SS.err
    Untracked:  code/subsetvcf_SS.out
    Untracked:  code/subsetvcf_noSS.err
    Untracked:  code/subsetvcf_noSS.out
    Untracked:  code/subsetvcf_pas.err
    Untracked:  code/subsetvcf_pas.out
    Untracked:  code/subsetvcf_perm.err
    Untracked:  code/subsetvcf_perm.out
    Untracked:  code/subsetvcf_rand.err
    Untracked:  code/subsetvcf_rand.out
    Untracked:  code/subtract5UTR.err
    Untracked:  code/subtract5UTR.out
    Untracked:  code/subtractExons.err
    Untracked:  code/subtractExons.out
    Untracked:  code/tabixSNPs.err
    Untracked:  code/tabixSNPs.out
    Untracked:  code/test.pdf
    Untracked:  code/testFix.txt
    Untracked:  code/test_verifybam.err
    Untracked:  code/test_verifybam.out
    Untracked:  code/tissuePAS2hg19.sh
    Untracked:  code/vcf_keepsnps.err
    Untracked:  code/vcf_keepsnps.out
    Untracked:  code/wrap_verifybam.err
    Untracked:  code/wrap_verifybam.out
    Untracked:  code/zipandtabPhen.err
    Untracked:  code/zipandtabPhen.out
    Untracked:  data/._.DS_Store
    Untracked:  data/._MetaDataSequencing.txt
    Untracked:  data/AnnotatedPAS/
    Untracked:  data/ApaByEgene/
    Untracked:  data/ApaByPgene/
    Untracked:  data/BadLines/
    Untracked:  data/BaseComp/
    Untracked:  data/Battle_pQTL/
    Untracked:  data/CheckSums/
    Untracked:  data/CompareOldandNew/
    Untracked:  data/DTmatrix/
    Untracked:  data/DiffIso/
    Untracked:  data/EncodeRNA/
    Untracked:  data/ExampleQTLPlots/
    Untracked:  data/ExampleQTLPlots_update/
    Untracked:  data/ExpressionIndependentapaQTLs.txt
    Untracked:  data/FiveMergedBW/
    Untracked:  data/FiveMergedBam/
    Untracked:  data/FlaggedPAS/
    Untracked:  data/GWAS_overlap/
    Untracked:  data/GeuvadisRNA/
    Untracked:  data/HMMqtls/
    Untracked:  data/LDSR_annotations/
    Untracked:  data/LZ_both/
    Untracked:  data/Li_eQTLs/
    Untracked:  data/NMD/
    Untracked:  data/NascentRNA/
    Untracked:  data/NucSpeceQTLeffect/
    Untracked:  data/PAS/
    Untracked:  data/PAS_postFlag/
    Untracked:  data/PolyA_DB/
    Untracked:  data/PreTerm_pheno/
    Untracked:  data/PrematureQTLNominal/
    Untracked:  data/PrematureQTLPermuted/
    Untracked:  data/QTLGenotypes/
    Untracked:  data/QTLoverlap/
    Untracked:  data/QTLoverlap_inclusive/
    Untracked:  data/QTLoverlap_nonNorm/
    Untracked:  data/README.md
    Untracked:  data/RNAseq/
    Untracked:  data/Reads2UTR/
    Untracked:  data/SNPinSS/
    Untracked:  data/SignalSiteFiles/
    Untracked:  data/TF_motifdisruption/
    Untracked:  data/TSS/
    Untracked:  data/ThirtyNineIndQtl_nominal/
    Untracked:  data/TissueData/
    Untracked:  data/Version15bp6As/
    Untracked:  data/Version15bp7As/
    Untracked:  data/apaQTLNominal/
    Untracked:  data/apaQTLNominal_4pc/
    Untracked:  data/apaQTLNominal_inclusive/
    Untracked:  data/apaQTLPermuted/
    Untracked:  data/apaQTLPermuted_4pc/
    Untracked:  data/apaQTLs/
    Untracked:  data/assignedPeaks/
    Untracked:  data/assignedPeaks_15Up/
    Untracked:  data/bam/
    Untracked:  data/bam_clean/
    Untracked:  data/bam_waspfilt/
    Untracked:  data/bed_10up/
    Untracked:  data/bed_clean/
    Untracked:  data/bed_clean_sort/
    Untracked:  data/bed_waspfilter/
    Untracked:  data/bedsort_waspfilter/
    Untracked:  data/bothFrac_FC/
    Untracked:  data/bw/
    Untracked:  data/bw_norm/
    Untracked:  data/eCLip/
    Untracked:  data/eQTL_LZ/
    Untracked:  data/eQTLs/
    Untracked:  data/exampleQTLs/
    Untracked:  data/exosome/
    Untracked:  data/fastq/
    Untracked:  data/filterPeaks/
    Untracked:  data/fourSU/
    Untracked:  data/h3k27ac/
    Untracked:  data/highdiffsiggenes.txt
    Untracked:  data/inclusivePeaks/
    Untracked:  data/inclusivePeaks_FC/
    Untracked:  data/intronRNAratio/
    Untracked:  data/intron_analysis/
    Untracked:  data/locusZoom/
    Untracked:  data/mergedBG/
    Untracked:  data/mergedBW_byfrac/
    Untracked:  data/mergedBW_norm/
    Untracked:  data/mergedBam/
    Untracked:  data/mergedbyFracBam/
    Untracked:  data/miRNAbinding/
    Untracked:  data/molPhenos/
    Untracked:  data/molQTLs/
    Untracked:  data/motifdistrupt/
    Untracked:  data/nPAS/
    Untracked:  data/netseq/
    Untracked:  data/nonNorm_pheno/
    Untracked:  data/nuc_10up/
    Untracked:  data/nuc_10upclean/
    Untracked:  data/oldPASfiles/
    Untracked:  data/overlapeQTL_try2/
    Untracked:  data/overlapeQTLs/
    Untracked:  data/pQTLoverlap/
    Untracked:  data/pacbio/
    Untracked:  data/peakCoverage/
    Untracked:  data/peaks_5perc/
    Untracked:  data/phenotype/
    Untracked:  data/phenotype_5perc/
    Untracked:  data/phenotype_inclusivePAS/
    Untracked:  data/phylop/
    Untracked:  data/pttQTL/
    Untracked:  data/pttQTLplots/
    Untracked:  data/sigDiffGenes.txt
    Untracked:  data/sort/
    Untracked:  data/sort_clean/
    Untracked:  data/sort_waspfilter/
    Untracked:  data/splicesite/
    Untracked:  data/twoMech/
    Untracked:  data/vareQTLvarAPAqtl/
    Untracked:  data/verifyBAM/
    Untracked:  data/verifyBAM_full/
    Untracked:  nohup.out
    Untracked:  output/._.DS_Store
    Untracked:  output/._AverageDiffHeatmap.Nuclear.png
    Untracked:  output/._AverageDiffHeatmap.Total.png
    Untracked:  output/._GeneswithAPApotential.png
    Untracked:  output/._GeneswithAPApotentialAllPAS.png
    Untracked:  output/._PASlocation.png
    Untracked:  output/._SignalSitePlot.png
    Untracked:  output/._meanCorrelationPhenotypes.svg
    Untracked:  output/._qqplot_Nuclear_APAperm.png
    Untracked:  output/._qqplot_Nuclear_APAperm_4pc.png
    Untracked:  output/._qqplot_Total_APAperm.png
    Untracked:  output/._qqplot_Total_APAperm_4pc.png
    Untracked:  output/AverageDiffHeatmap.Nuclear.png
    Untracked:  output/AverageDiffHeatmap.Total.png
    Untracked:  output/GeneswithAPApotential.png
    Untracked:  output/GeneswithAPApotentialAllPAS.png
    Untracked:  output/PASlocation.png
    Untracked:  output/SignalSitePlot.png
    Untracked:  output/SignalSitePlotbyLoc.png
    Untracked:  output/dtPlots/
    Untracked:  output/fastqc/
    Untracked:  output/meanCorrelationPhenotypes.svg
    Untracked:  output/newnuc.png
    Untracked:  output/newtot.png
    Untracked:  output/oldnuc.png
    Untracked:  output/oldtot.png
    Untracked:  output/qqplot_Nuclear_APAperm.png
    Untracked:  output/qqplot_Nuclear_APAperm_4pc.png
    Untracked:  output/qqplot_Total_APAperm.png
    Untracked:  output/qqplot_Total_APAperm_4pc.png
    Untracked:  run_verifybam517N.err
    Untracked:  run_verifybam517N.out

Unstaged changes:
    Modified:   analysis/ExploreNpas.Rmd
    Modified:   analysis/NuclearSpecIncludeNotTested.Rmd
    Modified:   analysis/PASdescriptiveplots.Rmd
    Modified:   analysis/Readdistagainstfeatures.Rmd
    Modified:   analysis/TSS.Rmd
    Modified:   analysis/decayAndStability.Rmd
    Modified:   analysis/miRNAdisrupt.Rmd
    Modified:   analysis/nascenttranscription.Rmd
    Modified:   analysis/nucSpecinEQTLs.Rmd
    Modified:   analysis/overlapapaqtlsandeqtls.Rmd
    Modified:   analysis/pQTLexampleplot.Rmd
    Modified:   analysis/propeQTLs_explained.Rmd
    Modified:   analysis/version15bpfilter.Rmd
    Modified:   code/DistPAS2Sig.py
    Modified:   code/Script4NuclearQTLexamples.sh
    Modified:   code/Script4TotalQTLexamples.sh
    Modified:   code/apaQTLsnake.err
    Modified:   code/environment.yaml
    Modified:   code/run_qtlFacetBoxplots.sh
    Deleted:    code/test.txt
    Deleted:    reads_graphs.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 fe3acb2 brimittleman 2020-02-18 add res
html 0fde09f brimittleman 2020-02-17 Build site.
Rmd f4a296f brimittleman 2020-02-17 add initial res for splice site 
library(workflowr)
This is workflowr version 1.6.0
Run ?workflowr for help getting started
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()
library(ggpubr)
Loading required package: magrittr

Attaching package: 'magrittr'
The following object is masked from 'package:purrr':

    set_names
The following object is masked from 'package:tidyr':

    extract

I will assess the 5’ splice site strength with maxentscore to see if this can tell us anything interesting about intronic polyadenylation.

http://hollywood.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html

How to use MaxEntScan::score5ss

Each sequence must be 9 bases long. [3 bases in exon][6 bases in intron] Input sequences as a FastA file with one sequence per line (no linebreaks). Non-ACGT sequences will not be processed.

Example Fasta File

> dummy1
cagGTAAGT
> dummy2 
gagGTAAGT
> dummy3 
taaATAAGT

I assigned PAS to introns. in https://brimittleman.github.io/apaQTL/nucintronicanalysis.html

pas2intron=read.table("../data/intron_analysis/IntronPeaksontoIntrons.bed",col.names = c("intronCHR", "intronStart", "intronEnd", "gene", "score", "strand", "peakCHR", "peakStart", "peakEnd", "PeakID", "meanUsage", "peakStrand")) 

#%>% mutate(PASloc=ifelse(strand=="+", peakEnd, peakStart)) %>% dplyr::select(intronStart, intronEnd, gene, strand, PeakID, PASloc ,meanUsage) %>% mutate(intronLength=intronEnd-intronStart , distance2PAS= ifelse(strand=="+", PASloc-intronStart, intronEnd-PASloc), propIntron=distance2PAS/intronLength)

I need a file with the PAS and the 5’ splice site. For negative strand the 5’ is the end and postitive strand PAS it is the start.

postive: start= start-3 end= start + 6

negative: start= end -6 end= end + 3

mkdir ../data/splicesite
PAS_5SS_pos= pas2intron %>% filter(strand=="+") %>% mutate(start=intronStart-3, end= intronStart +6) %>% select(intronCHR, start,end, PeakID,meanUsage, strand)
PAS_5SS_neg=pas2intron %>% filter(strand=="-") %>% mutate(start=intronEnd-6, end= intronEnd +3) %>% select(intronCHR, start,end, PeakID,meanUsage, strand)
PAS_5SS_both= PAS_5SS_neg %>% bind_rows(PAS_5SS_pos)



write.table(PAS_5SS_pos, "../data/splicesite/TestPosSS.bed", col.names = F, row.names = F, quote=F, sep="\t")

write.table(PAS_5SS_neg, "../data/splicesite/TestNegSS.bed", col.names = F, row.names = F, quote=F, sep="\t")


write.table(PAS_5SS_both, "../data/splicesite/AllPASSS.bed", col.names = F, row.names = F, quote=F, sep="\t")

Merge and sort these to get the nucleotides:

sort -k1,1 -k2,2n ../data/splicesite/AllPASSS.bed > ../data/splicesite/AllPASSS.sort.bed


#cut chr  

sed 's/^chr//' ../data/splicesite/AllPASSS.sort.bed >  ../data/splicesite/AllPASSS.sort.noChr.bed


#bedtools nuc

bedtools nuc -fi /project2/gilad/briana/genome_anotation_data/genome/Homo_sapiens.GRCh37.75.dna_sm.all.fa -bed ../data/splicesite/AllPASSS.sort.noChr.bed -seq -s > ../data/splicesite/AllPASSS.sort.Nuc.txt

This works and it flips the strand. the first 3 bases are the exon and the next 6 are the intron.

I need to turn this into a FA file. with the first 3 lower case and second 6 upper like the example. I can do this in python.

For each PAS i will have the name then the bases in the next

python splicesite2fasta.py

Score online with site and use Maximum Entropy Model.

splice result to keep every other line. Then I can join the reults with the initial bed.

python parseSSres.py
res=read.table("../data/splicesite/MaxIntResParsed.txt", col.names=c("splicesite", "maxentscore"), header=F, stringsAsFactors = F)

bothSS=read.table("../data/splicesite/AllPASSS.sort.noChr.bed", header = F, col.names = c("chr", 'start','end','PAS', "NuclearUsage", 'strand'))


bothandres=bothSS %>% bind_cols(res)

Plot usage and score:

cor.test(bothandres$NuclearUsage, bothandres$maxentscore)

    Pearson's product-moment correlation

data:  bothandres$NuclearUsage and bothandres$maxentscore
t = -3.547, df = 12534, p-value = 0.0003911
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 -0.04914437 -0.01416833
sample estimates:
        cor 
-0.03166605 
ggplot(bothandres, aes(x=maxentscore, y=NuclearUsage)) + geom_point() + geom_density2d(col="red")

Version Author Date
0fde09f brimittleman 2020-02-17

Filter usage higher (25%) and score above 0

bothandres_filt= bothandres %>% filter(NuclearUsage>0.25, maxentscore>0)

ggplot(bothandres_filt, aes(x=maxentscore, y=NuclearUsage)) + geom_point() + geom_density2d(col="red") + geom_smooth(method="lm")

Version Author Date
0fde09f brimittleman 2020-02-17

Does not look like there is a relationship here.

Expectation is a stronger 5’ SS means lower intronic usage. I will compare top 10% usage and bottom 10% usage

quantile(bothandres$NuclearUsage,probs=c(.1,.9))
       10%        90% 
0.05653846 0.37990385 
bothandres_topbottom = bothandres %>% filter(NuclearUsage<= 0.056 | NuclearUsage >=0.38) %>% mutate(Usage=ifelse(NuclearUsage <=.15, "Low","High"))

ggplot(bothandres_topbottom,aes(x=Usage, y=maxentscore))+ geom_boxplot()

bothandres_top=bothandres_topbottom %>% filter(Usage=="High")
bothandres_bottom=bothandres_topbottom %>% filter(Usage=="Low")

#x to the left of y  
wilcox.test(bothandres_top$maxentscore, bothandres_bottom$maxentscore, alternative="less")

    Wilcoxon rank sum test with continuity correction

data:  bothandres_top$maxentscore and bothandres_bottom$maxentscore
W = 681970, p-value = 0.00136
alternative hypothesis: true location shift is less than 0

top used have lower scores. This is in line with expectation.

Compare to a random set of splice sites. Select 12536

chroms=c("chr1", 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22')
allIntron=read.table("/project2/gilad/briana/apaQTL/data/intron_analysis/transcriptsMinusExons.sort.bed", col.names = c("chr","start","end", 'gene', 'score','strand'),header = T, stringsAsFactors = F) %>% filter(chr %in% chroms)

#sampleIntron= allIntron %>% sample_n(12536, replace = F)

Get the 5’ splice site for these:

#randPAS_5SS_pos= sampleIntron %>% filter(strand=="+") %>% mutate(newStart=start-3, newEnd= start +6) %>% select(chr, newStart,newEnd, gene,score, strand)



#randPAS_5SS_neg=sampleIntron %>% filter(strand=="-") %>% mutate(newStart=end-6, newEnd= end +3) %>% select(chr, newStart,newEnd, gene,score, strand)


#randPAS_both= randPAS_5SS_pos %>% bind_rows(randPAS_5SS_neg)


#write.table(randPAS_both,"../data/splicesite/RandomIntronSS.bed",sep="\t", col.names = F, row.names = F, quote = F)
sort -k1,1 -k2,2n ../data/splicesite/RandomIntronSS.bed | sed 's/^chr//' > ../data/splicesite/RandomIntronSS_noChr.bed



#bedtools nuc

bedtools nuc -fi /project2/gilad/briana/genome_anotation_data/genome/Homo_sapiens.GRCh37.75.dna_sm.all.fa -bed ../data/splicesite/RandomIntronSS_noChr.bed -seq -s > ../data/splicesite/RandomIntronSS_noChr.Nuc.bed


python Randomsplicesite2fasta.py

python parseRanodmSSres.py

Eval:

RandomSites=read.table("../data/splicesite/RandomIntronSS.bed",col.names = c('chr','start','end','name','score','strand'))
RandomRes= read.table("../data/splicesite/RandomSSMaxentParsed.txt", col.names = c("splicesite", "maxentscore_cont"), stringsAsFactors = F, header = F)

RandomSitewRes=RandomSites %>% bind_cols(RandomRes)

Compare these to the actual:

RealandCont=as.data.frame(cbind(Control=RandomSitewRes$maxentscore_cont, PAS=bothandres$maxentscore))
RealandContG=RealandCont %>%  gather("set", "score")
ggplot(RealandContG, aes(x=set, y = score,fill=set)) + geom_boxplot() + stat_compare_means()

summary(RandomSitewRes$maxentscore_cont)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
-45.450   7.070   8.620   7.477   9.800  11.810 
summary(bothandres$maxentscore)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
-47.350   7.298   8.760   6.872   9.990  11.810 
wilcox.test(RandomSitewRes$maxentscore_cont,bothandres$maxentscore, alternative = "less")

    Wilcoxon rank sum test with continuity correction

data:  RandomSitewRes$maxentscore_cont and bothandres$maxentscore
W = 74942000, p-value = 1.133e-10
alternative hypothesis: true location shift is less than 0

This is not as informative as the above analysis based on usage.

Test if any of the QTLs fall in 5’ splice sites. For this I will look at the 5’ site for every intron:

allIntron_sspos= allIntron %>% filter(strand=="+") %>% mutate(newStart=start-3, newEnd= start +6) %>% select(chr, newStart,newEnd, gene,score, strand)
allIntron_ssneg= allIntron  %>% filter(strand=="-") %>% mutate(newStart=end-6, newEnd= end +3) %>% select(chr, newStart,newEnd, gene,score, strand)

AllIntron_both=allIntron_ssneg %>% bind_rows(allIntron_sspos)

write.table(AllIntron_both, "../data/splicesite/AllIntron5primeSS.bed", col.names = F, row.names = F, quote = F, sep="\t")

sort and intersect with qtl snps.


sort -k1,1 -k2,2n ../data/splicesite/AllIntron5primeSS.bed| sed 's/^chr//' > ../data/splicesite/AllIntron5primeSS_sort.bed

sort -k1,1 -k2,2n ../data/apaQTLs/Nuclear_apaQTLs4pc_5fdr.WITHSTRAND.bed | sed '1d' | head -n -1 > ../data/apaQTLs/Nuclear_apaQTLs4pc_5fdr.WITHSTRAND.sort.bed

bedtools intersect -wo -a ../data/splicesite/AllIntron5primeSS_sort.bed -b ../data/apaQTLs/Nuclear_apaQTLs4pc_5fdr.WITHSTRAND.sort.bed -s > ../data/splicesite/QTLin5SS.txt

1 example.

15 31229459 31229468 FAN1 . + 15 31229462 31229463 FAN1:peak42822:utr3 83 + 1


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] ggpubr_0.2      magrittr_1.5    forcats_0.3.0   stringr_1.3.1  
 [5] dplyr_0.8.0.1   purrr_0.3.2     readr_1.3.1     tidyr_0.8.3    
 [9] tibble_2.1.1    ggplot2_3.1.1   tidyverse_1.2.1 workflowr_1.6.0

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5 haven_1.1.2      lattice_0.20-38  colorspace_1.3-2
 [5] generics_0.0.2   htmltools_0.3.6  yaml_2.2.0       rlang_0.4.0     
 [9] later_0.7.5      pillar_1.3.1     glue_1.3.0       withr_2.1.2     
[13] modelr_0.1.2     readxl_1.1.0     plyr_1.8.4       munsell_0.5.0   
[17] gtable_0.2.0     cellranger_1.1.0 rvest_0.3.2      evaluate_0.12   
[21] labeling_0.3     knitr_1.20       httpuv_1.4.5     highr_0.7       
[25] broom_0.5.1      Rcpp_1.0.2       promises_1.0.1   scales_1.0.0    
[29] backports_1.1.2  jsonlite_1.6     fs_1.3.1         hms_0.4.2       
[33] digest_0.6.18    stringi_1.2.4    grid_3.5.1       rprojroot_1.3-2 
[37] cli_1.1.0        tools_3.5.1      lazyeval_0.2.1   crayon_1.3.4    
[41] whisker_0.3-2    pkgconfig_2.0.2  MASS_7.3-51.1    xml2_1.2.0      
[45] lubridate_1.7.4  assertthat_0.2.0 rmarkdown_1.10   httr_1.3.1      
[49] rstudioapi_0.10  R6_2.3.0         nlme_3.1-137     git2r_0.26.1    
[53] compiler_3.5.1