Last updated: 2020-02-05
Checks: 7 0
Knit directory: apaQTL/analysis/
This reproducible R Markdown analysis was created with workflowr (version 1.5.0). 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(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.
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/logs/
Ignored: data/.DS_Store
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/._DistPAS2Sig_RandomIntron.py
Untracked: code/._EandPqtl_perm.sh
Untracked: code/._EandPqtls.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/._RNAbam2bw.sh
Untracked: code/._RNAseqDTplot.sh
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/._extractGenotypes.py
Untracked: code/._extractPACmeanPhyloP.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/._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/._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/._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/._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/._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/._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/DistPAS2Sig_RandomIntron.py
Untracked: code/EandPqtl.err
Untracked: code/EandPqtl.out
Untracked: code/EncodeRNADTPlotGeneRegions.err
Untracked: code/EncodeRNADTPlotGeneRegions.out
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/README.md
Untracked: code/RNABam2BW.err
Untracked: code/RNABam2BW.out
Untracked: code/RNAseqDTPlotGeneRegions.err
Untracked: code/RNAseqDTPlotGeneRegions.out
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/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/extractPACmeanPhyloP.py
Untracked: code/fixExandUnexeQTL
Untracked: code/fix_randomIntron.py
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/log/
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/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/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/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/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/test_verifybam.err
Untracked: code/test_verifybam.out
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/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/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/eQTLs/
Untracked: data/exampleQTLs/
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/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/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/NuclearSpecIncludeNotTested.Rmd
Modified: analysis/PASdescriptiveplots.Rmd
Modified: analysis/RNAbinding.Rmd
Modified: analysis/Readdistagainstfeatures.Rmd
Modified: analysis/TSS.Rmd
Modified: analysis/decayAndStability.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/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 | a1f5355 | brimittleman | 2020-02-05 | add potential mechanisms and ld scripts |
| html | 3d9f5c7 | brimittleman | 2020-01-31 | Build site. |
| Rmd | fd5ccd7 | brimittleman | 2020-01-31 | add LD regress notes and first var in apa |
library(workflowr)This is workflowr version 1.5.0
Run ?workflowr for help getting startedlibrary(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()LD score regression with apaQTLs and multiple myeloma?
https://www.nature.com/articles/s41467-018-04989-w
QTLs:
Region around permuted snps. 500bp
try a few different
PAS:
maybe 1000 base pairs around each PAS.
bed file chrom start and end. - use CHR
-b cells: lymphocite
GWAS atlas
http://www.computationalmedicine.fi/data#Cytokine_GWAS
GWAS from Phenix= /project2/yangili1/zpmu/GWAS_loci/27863252
sle_Vyse_chr1-22.txt.gz
RA_GWASmeta_TransEthnic_v2.txt.gz
http://www.nealelab.is/uk-biobank - myeloma and luekemias
HG 19 LD scores
03,05,06,07
/project2/yangili1/zpmu/ldsc/scripts
First I will prepare the PAS and apaQTL filese:
mkdir ../data/LDSR_annotationsNuclear 5% PAS
PAS=read.table("../data/PAS/APApeak_Peaks_GeneLocAnno.Nuclear.5perc.sort.bed",col.names = c("Chr","start","end","name","score","stand"),stringsAsFactors = F)
PAS_500=PAS%>% mutate(chrom=paste("chr", Chr, sep=""),newStart=end-250, newEnd=end+250 ) %>% select(chrom,newStart,newEnd)
PAS_1000=PAS%>% mutate(chrom=paste("chr", Chr, sep=""),newStart=end-1000, newEnd=end+1000 ) %>% select(chrom, newStart,newEnd)write.table(PAS_500,"../data/LDSR_annotations/PAS_Nuclear500.bed", col.names = F, row.names = F, quote = F, sep="\t")
write.table(PAS_1000,"../data/LDSR_annotations/PAS_Nuclear1000.bed", col.names = F, row.names = F, quote = F, sep="\t")Sort:
sort -k1,1 -k2,2n ../data/LDSR_annotations/PAS_Nuclear500.bed > ../data/LDSR_annotations/PAS_Nuclear500.sort.bed
sort -k1,1 -k2,2n ../data/LDSR_annotations/PAS_Nuclear1000.bed > ../data/LDSR_annotations/PAS_Nuclear1000.sort.bedQTLS:
RSID=read.table("../../../briana/li_genotypes/RSID2snploc.txt", header = T, stringsAsFactors = F, col.names = c("snp","sid", "ref","alt"))
NucQTL=read.table("../data/apaQTLPermuted_4pc/APApeak_Phenotype_GeneLocAnno.Nuclear_permResBH.txt", header = T ,stringsAsFactors = F) %>% inner_join(RSID, by="sid") %>% separate(snp, into=c("chr","loc"),sep=":")
NucQTL500=NucQTL%>% mutate(start=as.integer(loc)-250,end=as.integer(loc)+250, chrom=paste("chr",chr,by="")) %>% select(chrom,start,end)
NucQTL1000=NucQTL%>% mutate(start=as.integer(loc)-500,end=as.integer(loc)+500, chrom=paste("chr",chr,by="")) %>% select(chrom,start,end)write.table(NucQTL500,"../data/LDSR_annotations/QTL_Nuclear500.bed", col.names = F, row.names = F, quote = F, sep="\t")
write.table(NucQTL1000,"../data/LDSR_annotations/QTL_Nuclear1000.bed", col.names = F, row.names = F, quote = F, sep="\t")Sort:
sort -k1,1 -k2,2n ../data/LDSR_annotations/QTL_Nuclear500.bed > ../data/LDSR_annotations/QTL_Nuclear500.sort.bed
sort -k1,1 -k2,2n ../data/LDSR_annotations/QTL_Nuclear1000.bed > ../data/LDSR_annotations/QTL_Nuclear1000.sort.bedChoose test gwas:
Start with RA because it works with Phenoix’s code.
I moved the scripts to my code directory. I will make a copy of it for PAS_500_Lymph
cp -R scripts scripts_PAS_500_Lymph
../data/LDSR_annotations/
Change the places in 03,05,06,07
#03 will annotate all 4 of these
sbatch scripts_PAS_500_Lymph/03_immuneAtlas_annot.sh
sbatch scripts_PAS_500_Lymph/05_immuneAtlas_ldscore.sh
sbatch scripts_PAS_500_Lymph/06_munge_gwas_lymphPAS500.sh
mkdir /project2/gilad/briana/apaQTL/data/LDSR_annotations/results/
sbatch scripts_PAS_500_Lymph/07_partition_h2g.sh stuck on 7. need baseline LD files
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 workflowr_1.5.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 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 tools_3.5.1
[9] digest_0.6.18 lubridate_1.7.4 jsonlite_1.6 evaluate_0.12
[13] nlme_3.1-137 gtable_0.2.0 lattice_0.20-38 pkgconfig_2.0.2
[17] rlang_0.4.0 cli_1.1.0 rstudioapi_0.10 yaml_2.2.0
[21] haven_1.1.2 withr_2.1.2 xml2_1.2.0 httr_1.3.1
[25] knitr_1.20 hms_0.4.2 generics_0.0.2 fs_1.3.1
[29] rprojroot_1.3-2 grid_3.5.1 tidyselect_0.2.5 glue_1.3.0
[33] R6_2.3.0 readxl_1.1.0 rmarkdown_1.10 modelr_0.1.2
[37] magrittr_1.5 whisker_0.3-2 backports_1.1.2 scales_1.0.0
[41] promises_1.0.1 htmltools_0.3.6 rvest_0.3.2 assertthat_0.2.0
[45] colorspace_1.3-2 httpuv_1.4.5 stringi_1.2.4 lazyeval_0.2.1
[49] munsell_0.5.0 broom_0.5.1 crayon_1.3.4