Last updated: 2019-09-04
Checks: 2 0
Knit directory: apaQTL/analysis/
This reproducible R Markdown analysis was created with workflowr (version 1.4.0). 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! 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/mergedBW_byfrac/
Ignored: docs/.DS_Store
Ignored: docs/figure/.DS_Store
Ignored: output/.DS_Store
Untracked files:
Untracked: .Rprofile
Untracked: ._.DS_Store
Untracked: .gitignore
Untracked: @
Untracked: _workflowr.yml
Untracked: analysis/._PASdescriptiveplots.Rmd
Untracked: analysis/._cuttoffPercUsage.Rmd
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/totalspec.Rmd
Untracked: apaQTL.Rproj
Untracked: code/.NascentRNAdtPlotFirstintronicPAS.sh.swp
Untracked: code/._ApaQTL_nominalNonnorm.sh
Untracked: code/._BothFracDTPlotGeneRegions.sh
Untracked: code/._BothFracDTPlotGeneRegions_normalized.sh
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/._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/._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/._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/._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_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/._extractGenotypes.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/._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/._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/._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_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/._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/._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_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/ApaQTL_nominalNonnorm.sh
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/BothFracDTPlotGeneRegions_normalized.sh
Untracked: code/DistPAS2Sig.py
Untracked: code/EandPqtl.err
Untracked: code/EandPqtl.out
Untracked: code/EandPqtl_perm.sh
Untracked: code/EandPqtls.sh
Untracked: code/EncodeRNADTPlotGeneRegions.err
Untracked: code/EncodeRNADTPlotGeneRegions.out
Untracked: code/FC_NucintornUpandDown.sh
Untracked: code/FC_NucintronPASupandDown.err
Untracked: code/FC_NucintronPASupandDown.out
Untracked: code/FC_UTR.err
Untracked: code/FC_UTR.out
Untracked: code/FC_UTR.sh
Untracked: code/FC_intornUpandDownsteamPAS.sh
Untracked: code/FC_intronPASupandDown.err
Untracked: code/FC_intronPASupandDown.out
Untracked: code/FC_nascent.err
Untracked: code/FC_nascentout
Untracked: code/FC_nascentseq.sh
Untracked: code/FC_newPAS_olddata.err
Untracked: code/FC_newPAS_olddata.out
Untracked: code/FC_newPeaks_olddata.sh
Untracked: code/HMMpermuteTotal.py
Untracked: code/HmmPermute.p
Untracked: code/HmmPermute.py
Untracked: code/IntronicPASDT.err
Untracked: code/IntronicPASDT.out
Untracked: code/IntronicPASDT.sh
Untracked: code/LC_samplegroups.py
Untracked: code/LD_qtl.sh
Untracked: code/LD_snpsproxy.sh
Untracked: code/LD_vcftools.hap.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/NascentRNAdtPlot.sh
Untracked: code/NascentRNAdtPlot3UTRPAS.sh
Untracked: code/NascentRNAdtPlotExcludeFirstintronicPAS.sh
Untracked: code/NascentRNAdtPlotFirstintronicPAS.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/Nuclear_example.err
Untracked: code/Nuclear_example.out
Untracked: code/PACbioDT.err
Untracked: code/PACbioDT.out
Untracked: code/PACbioDTitronic.err
Untracked: code/PACbioDTitronic.out
Untracked: code/PTTfacetboxplots.R
Untracked: code/PrematureQTLNominal.sh
Untracked: code/PrematureQTLPermuted.sh
Untracked: code/Prematureqtl_nominal.err
Untracked: code/Prematureqtl_nominal.out
Untracked: code/Prematureqtl_permuted.err
Untracked: code/Prematureqtl_permuted.out
Untracked: code/QTL2bed.py
Untracked: code/QTL2bed_withstrand.py
Untracked: code/README.md
Untracked: code/RNABam2BW.err
Untracked: code/RNABam2BW.out
Untracked: code/RNAbam2bw.sh
Untracked: code/RNAseqDTPlotGeneRegions.err
Untracked: code/RNAseqDTPlotGeneRegions.out
Untracked: code/RNAseqDTplot.sh
Untracked: code/Rplots.pdf
Untracked: code/SAF215upbed.py
Untracked: code/SAF215upbed_gen.py
Untracked: code/Script4NuclearPTTqtlexamples.sh
Untracked: code/Script4NuclearQTLexamples.sh
Untracked: code/Script4TotalPTTqtlexamples.sh
Untracked: code/Script4TotalQTLexamples.sh
Untracked: code/TESplots100bp.err
Untracked: code/TESplots100bp.out
Untracked: code/TESplots100bp.sh
Untracked: code/TESplots150bp.err
Untracked: code/TESplots150bp.out
Untracked: code/TESplots150bp.sh
Untracked: code/TESplots200bp.err
Untracked: code/TESplots200bp.out
Untracked: code/TESplots200bp.sh
Untracked: code/TotalPAS_5perc.bed.py
Untracked: code/Total_example.err
Untracked: code/Total_example.out
Untracked: code/Untitled
Untracked: code/Upstream100Bases_general.py
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/ZipandTabPheno.sh
Untracked: code/aAPAqtl_nominal39ind.sh
Untracked: code/annotatePacBioPASregion.sh
Untracked: code/annotatedPAS2bed.py
Untracked: code/annotatedPASregion.err
Untracked: code/annotatedPASregion.out
Untracked: code/apaInPandE.py
Untracked: code/apaQTLCorrectPvalMakeQQ_4pc.R
Untracked: code/apaQTLCorrectpval_6or7a.R
Untracked: code/apaQTL_Nominal_4pc.sh
Untracked: code/apaQTL_nominalv67.sh
Untracked: code/apaQTL_permuted.4pc.sh
Untracked: code/apaQTL_permuted_test6A7A.sh
Untracked: code/apafacetboxplots.R
Untracked: code/apainRibo.py
Untracked: code/apaqtlfacetboxplots.R
Untracked: code/assignNucIntonpeak2intronlocs.sh
Untracked: code/assignPeak2Intronicregion.err
Untracked: code/assignPeak2Intronicregion.out
Untracked: code/assignTotIntronpeak2intronlocs.sh
Untracked: code/assigntotPeak2Intronicregion.err
Untracked: code/assigntotPeak2Intronicregion.out
Untracked: code/bam2BW_5primemost.sh
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/bothFracDTplot1stintron.sh
Untracked: code/bothFracDTplot4thintron.sh
Untracked: code/bothFrac_FC.err
Untracked: code/bothFrac_FC.out
Untracked: code/bothFrac_FC.sh
Untracked: code/callSHscripts.txt
Untracked: code/changePermQTLres2geneName.py
Untracked: code/changeRibonomQTLres2genename.py
Untracked: code/changenomQTLres2geneName.py
Untracked: code/chooseAnno2PAS_pacbio.py
Untracked: code/closestannotated.err
Untracked: code/closestannotated.out
Untracked: code/closestannotated.sh
Untracked: code/closestannotated_byfrac.sh
Untracked: code/closestannotatedbyfrac.err
Untracked: code/closestannotatedbyfrac.out
Untracked: code/codingdms2bed.py
Untracked: code/convertNominal2SNPLOC.py
Untracked: code/convertNominal2SNPloc2Versions.py
Untracked: code/correctNomeqtl.R
Untracked: code/createPlinkSampfile.py
Untracked: code/dag.pdf
Untracked: code/dagPAS.pdf
Untracked: code/dagfiltPAS.pdf
Untracked: code/eQTL_switch2snploc.py
Untracked: code/eQTLgenestestedapa.py
Untracked: code/encodeRNADTplots.sh
Untracked: code/environmentLeaf.yaml
Untracked: code/extractGenotypes.py
Untracked: code/extractseqfromqtlfastq.py
Untracked: code/fc2leafphen.py
Untracked: code/fc_filteredPAS6and7As.sh
Untracked: code/fifteenBPupstreamPAS.py
Untracked: code/fiftyBPupstreamPAS.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/filterSAFforMP_gen.py
Untracked: code/finalPASbed2SAF.py
Untracked: code/findbuginpeaks.R
Untracked: code/fix4su304corr.py
Untracked: code/fix4su604corr.py
Untracked: code/fix4sukalisto.py
Untracked: code/fixExandUnexeQTL
Untracked: code/fixExandUnexeQTL.py
Untracked: code/fixFChead_bothfrac.py
Untracked: code/fixFChead_short.py
Untracked: code/fixFChead_summary.py
Untracked: code/fixH3k12ac.py
Untracked: code/fixPASregionSNPs.py
Untracked: code/fixRNAhead4corr.py
Untracked: code/fixRNAkalisto.py
Untracked: code/fixgroupedtranscript.py
Untracked: code/fixhead_netseqfc.py
Untracked: code/genotypesYRI.gen.proc.keep.vcf.log
Untracked: code/genotypesYRI.gen.proc.keep.vcf.recode.vcf
Untracked: code/get100upPAS.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/getSeq100up.sh
Untracked: code/getUpstreamIntronNuclear.py
Untracked: code/getseq100up.err
Untracked: code/getseq100up.out
Untracked: code/grouptranscripts.err
Untracked: code/grouptranscripts.out
Untracked: code/grouptranscripts.py
Untracked: code/intersectPAS_ssSNPS.err
Untracked: code/intersectPAS_ssSNPS.out
Untracked: code/intersectVCFPAS.err
Untracked: code/intersectVCFPAS.out
Untracked: code/intersectVCFandupPAS.sh
Untracked: code/keep5perMAF.py
Untracked: code/keepSNP_vcf.sh
Untracked: code/log/
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/mergeBW_norm.sh
Untracked: code/mergeBWnorm.err
Untracked: code/mergeBWnorm.out
Untracked: code/mergeBamNacent.err
Untracked: code/mergeBamNacent.out
Untracked: code/mergeBamNascent.sh
Untracked: code/mergeRNAbam.err
Untracked: code/mergeRNAbam.out
Untracked: code/mnase1stintron.sh
Untracked: code/mnaseDTPlot1stintron.err
Untracked: code/mnaseDTPlot1stintron.out
Untracked: code/mnaseDTPlot4thintron.err
Untracked: code/mnaseDTPlot4thintron.out
Untracked: code/mnaseDT_fourthintron.sh
Untracked: code/netDTPlot4thintron.out
Untracked: code/netseqDTplot1stIntron.sh
Untracked: code/netseqFC.err
Untracked: code/netseqFC.out
Untracked: code/netseqFC.sh
Untracked: code/neyDTPlot4thintron.err
Untracked: code/nucQTLGWAS.py
Untracked: code/nucQTLGWAS_withLD.py
Untracked: code/nucSpecQTLineData.py
Untracked: code/nucSpeceffectsize.py
Untracked: code/pQTLsotherdata.py
Untracked: code/pacbioDT.sh
Untracked: code/pacbioIntronicDT.sh
Untracked: code/parseBestbamid.py
Untracked: code/phenoQTLfromlist.py
Untracked: code/plink.log
Untracked: code/processYRIgen.py
Untracked: code/prxySNP.err
Untracked: code/prxySNP.out
Untracked: code/pttFacetBoxplots.err
Untracked: code/pttFacetBoxplots.out
Untracked: code/pttQTLsinapaQTL.py
Untracked: code/pullTwoMechData.py
Untracked: code/qtlFacetBoxplots.err
Untracked: code/qtlFacetBoxplots.out
Untracked: code/qtlRegionseq.sh
Untracked: code/qtlsPvalOppFrac.py
Untracked: code/rLD_vcftools.hap.err
Untracked: code/removeXfromHmm.py
Untracked: code/removeloc_pheno.py
Untracked: code/riboQTL.sh
Untracked: code/riboqtl.err
Untracked: code/riboqtl.out
Untracked: code/runBestBamID.err
Untracked: code/runCorrectNomEqtl.sh
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/runHMMpermuteAPAqtls.sh
Untracked: code/runHMMpermuteeQTLS.sh
Untracked: code/runHMMpermuteeQTLs.err
Untracked: code/runHMMpermuteeQTLs.out
Untracked: code/runMakeEmpiricaleQTL_unexp.sh
Untracked: code/runMakeEmpiricaleQTLs.err
Untracked: code/runMakeEmpiricaleQTLs.out
Untracked: code/runMakeEmpiricaleQTLsunex.err
Untracked: code/runMakeEmpiricaleQTLsunex.out
Untracked: code/runMakeeQTLempirical.sh
Untracked: code/run_DistPAS2Sig.err
Untracked: code/run_DistPAS2Sig.out
Untracked: code/run_bam2bw.err
Untracked: code/run_bam2bw.out
Untracked: code/run_bam2bw_all3prime.sh
Untracked: code/run_bam2bw_extra3.sh
Untracked: code/run_bam2bwexta.err
Untracked: code/run_bam2bwexta.out
Untracked: code/run_bestbamid.sh
Untracked: code/run_distPAS2Sig.sh
Untracked: code/run_filtersnpLD.sh
Untracked: code/run_getAPAfromanyeQTL.err
Untracked: code/run_getAPAfromanyeQTL.out
Untracked: code/run_getAPAfromeQTL_version6.7.sh
Untracked: code/run_getApaPval4eQTLs.err
Untracked: code/run_getApaPval4eQTLs.out
Untracked: code/run_getApaPval4eQTLsunexplained.err
Untracked: code/run_getApaPval4eQTLsunexplained.out
Untracked: code/run_getApaPval4eqtl.sh
Untracked: code/run_getapafromeQTL.sh
Untracked: code/run_getapapval4eqtl_unexp.sh
Untracked: code/run_leafcutterDiffIso.sh
Untracked: code/run_leafcutter_ds.err
Untracked: code/run_leafcutter_ds.out
Untracked: code/run_prxySNP.sh
Untracked: code/run_pttfacetboxplot.sh
Untracked: code/run_qtlFacetBoxplots.sh
Untracked: code/run_sepUsagephen.sh
Untracked: code/run_sepgenobychrom.err
Untracked: code/run_sepgenobychrom.out
Untracked: code/run_sepgenobychrom.sh
Untracked: code/run_sepusage.err
Untracked: code/run_sepusage.out
Untracked: code/run_verifybam.err
Untracked: code/run_verifybam.out
Untracked: code/run_verifybam.sh
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/run_verifybam_fullVCF.sh
Untracked: code/runprxySNP.err
Untracked: code/runprxySNP.out
Untracked: code/selectNominalPvalues.py
Untracked: code/sepUsagePhen.py
Untracked: code/sepgenobychrom.py
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/sortindexRNAbam.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_SS.err
Untracked: code/subsetvcf_SS.out
Untracked: code/subsetvcf_noSS.err
Untracked: code/subsetvcf_noSS.out
Untracked: code/subsetvcf_otherreg.sh
Untracked: code/subsetvcf_pas.err
Untracked: code/subsetvcf_pas.out
Untracked: code/subsetvcf_perm.err
Untracked: code/subsetvcf_perm.out
Untracked: code/subsetvcf_permSS.sh
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/subtractExons.sh
Untracked: code/subtractfiveprimeUTR.sh
Untracked: code/tabixSNPS.sh
Untracked: code/tabixSNPs.err
Untracked: code/tabixSNPs.out
Untracked: code/tenBPupstreamPAS.py
Untracked: code/testVerifyBam.sh
Untracked: code/test_verifybam.err
Untracked: code/test_verifybam.out
Untracked: code/totSeceffectsize.py
Untracked: code/transcriptdm2bed.py
Untracked: code/twentyBPupstreamPAS.py
Untracked: code/utrdms2saf.py
Untracked: code/vcf2bed.py
Untracked: code/vcf_keepsnps.err
Untracked: code/vcf_keepsnps.out
Untracked: code/verifyBam18517N.sh
Untracked: code/verifyBam18517T.sh
Untracked: code/verifyBam19128N.sh
Untracked: code/verifyBam19128T.sh
Untracked: code/wrap_verifybam.err
Untracked: code/wrap_verifybam.out
Untracked: code/wrap_verifybam.sh
Untracked: code/wrap_verifybam_full.sh
Untracked: code/writeExampleQTLcode.py
Untracked: code/writePTTexamplecode.py
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/Battle_pQTL/
Untracked: data/CheckSums/
Untracked: data/CompareOldandNew/
Untracked: data/DTmatrix/
Untracked: data/DiffIso/
Untracked: data/EncodeRNA/
Untracked: data/ExampleQTLPlots/
Untracked: data/FlaggedPAS/
Untracked: data/GWAS_overlap/
Untracked: data/GeuvadisRNA/
Untracked: data/HMMqtls/
Untracked: data/Li_eQTLs/
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_nonNorm/
Untracked: data/README.md
Untracked: data/RNAseq/
Untracked: data/Reads2UTR/
Untracked: data/SNPinSS/
Untracked: data/SignalSiteFiles/
Untracked: data/TF_motifdisruption/
Untracked: data/ThirtyNineIndQtl_nominal/
Untracked: data/Version15bp6As/
Untracked: data/Version15bp7As/
Untracked: data/apaQTLNominal/
Untracked: data/apaQTLNominal_4pc/
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/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_norm/
Untracked: data/mergedBam/
Untracked: data/mergedbyFracBam/
Untracked: data/molPhenos/
Untracked: data/molQTLs/
Untracked: data/motifdistrupt/
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/pttQTL/
Untracked: data/pttQTLplots/
Untracked: data/sigDiffGenes.txt
Untracked: data/sort/
Untracked: data/sort_clean/
Untracked: data/sort_waspfilter/
Untracked: data/twoMech/
Untracked: data/verifyBAM/
Untracked: data/verifyBAM_full/
Untracked: docs/._.DS_Store
Untracked: docs/figure/._.DS_Store
Untracked: docs/figure/nonNormQTL.Rmd/._figure2D-1.pdf
Untracked: nohup.out
Untracked: output/._.DS_Store
Untracked: output/._meanCorrelationPhenotypes.svg
Untracked: output/dtPlots/
Untracked: output/fastqc/
Untracked: output/meanCorrelationPhenotypes.svg
Untracked: run_verifybam517N.err
Untracked: run_verifybam517N.out
Unstaged changes:
Modified: analysis/NuclearSpecAPAqtl.Rmd
Modified: analysis/PrematureTermQTL.Rmd
Modified: analysis/Readdistagainstfeatures.Rmd
Modified: analysis/compareAnnotatedpas.Rmd
Modified: analysis/overlapapaqtlsandeqtls.Rmd
Modified: analysis/rerunQTL_changePC.Rmd
Modified: analysis/version15bpfilter.Rmd
Modified: code/BothFracDTPlotGeneRegions.sh
Modified: code/Snakefile
Modified: code/SnakefilefiltPAS
Modified: code/apaQTLCorrectPvalMakeQQ.R
Modified: code/apaQTL_Nominal.sh
Modified: code/apaQTL_permuted.sh
Modified: code/apaQTLsnake.err
Modified: code/bam2bw.sh
Modified: code/bed2saf.py
Modified: code/cluster.json
Modified: code/clusterfiltPAS.json
Modified: code/config.yaml
Modified: code/environment.yaml
Modified: code/makePheno.py
Modified: code/mergeAllBam.sh
Modified: code/mergeByFracBam.sh
Modified: code/mergePeaks.sh
Modified: code/peakFC.sh
Modified: code/snakemake.batch
Modified: code/snakemakePAS.batch
Modified: code/snakemakefiltPAS.batch
Modified: code/submit-snakemake.sh
Modified: code/submit-snakemakePAS.sh
Modified: code/submit-snakemakefiltPAS.sh
Deleted: code/test.txt
Modified: data/MetaDataSequencing.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 | 5984fad | brimittleman | 2019-09-04 | update for new filter condition |
| html | 07d9709 | brimittleman | 2019-08-28 | Build site. |
| Rmd | d5f19cc | brimittleman | 2019-08-28 | add new QC files to index |
| html | 4cd5f28 | brimittleman | 2019-08-26 | Build site. |
| Rmd | 5289aa1 | brimittleman | 2019-08-26 | add extra MP qc |
| html | 191d71f | brimittleman | 2019-08-07 | Build site. |
| Rmd | 01d0be5 | brimittleman | 2019-08-07 | add reads_graph analysis |
| html | d13025b | brimittleman | 2019-07-31 | Build site. |
| Rmd | e2ff61a | brimittleman | 2019-07-31 | add mayher plot to site |
| html | 33a700a | brimittleman | 2019-07-25 | Build site. |
| Rmd | f3e3e16 | brimittleman | 2019-07-25 | small edits from paper writing and add gwas analysis |
| html | fb1fde6 | brimittleman | 2019-07-16 | Build site. |
| Rmd | 2572d13 | brimittleman | 2019-07-16 | add compare annotated and additional coverage |
| html | 272b0b4 | brimittleman | 2019-07-08 | Build site. |
| Rmd | b1e6dd1 | brimittleman | 2019-07-08 | update ptt analysis |
| html | 5566d80 | brimittleman | 2019-07-07 | Build site. |
| Rmd | f85f6d0 | brimittleman | 2019-07-07 | add ptt eqtls |
| html | 2fb467b | brimittleman | 2019-07-07 | Build site. |
| Rmd | bd5f228 | brimittleman | 2019-07-07 | add nuc spec eqtl res |
| html | a4a34bf | brimittleman | 2019-07-01 | Build site. |
| html | 5edd9c7 | brimittleman | 2019-06-30 | Build site. |
| Rmd | 709b4c8 | brimittleman | 2019-06-30 | add two reg |
| html | da5807e | brimittleman | 2019-06-28 | Build site. |
| html | 1e58d07 | brimittleman | 2019-06-27 | Build site. |
| Rmd | db5d2e6 | brimittleman | 2019-06-27 | add pqtl example |
| html | 5d97550 | brimittleman | 2019-06-25 | Build site. |
| Rmd | 3e288f8 | brimittleman | 2019-06-25 | add tf analysis |
| html | 433092b | brimittleman | 2019-06-24 | Build site. |
| Rmd | 78dd5da | brimittleman | 2019-06-24 | add snp in ss analysis |
| html | fcab450 | brimittleman | 2019-06-21 | Build site. |
| Rmd | 5c83496 | brimittleman | 2019-06-21 | fix html typo |
| html | cd60f50 | brimittleman | 2019-06-20 | Build site. |
| Rmd | 6df08b6 | brimittleman | 2019-06-20 | change analysis to include not tested in total as nuc spec |
| html | 529a38a | brimittleman | 2019-06-18 | Build site. |
| html | b3328b6 | brimittleman | 2019-06-18 | Build site. |
| Rmd | 01bc8aa | brimittleman | 2019-06-18 | add verify first inton res |
| html | 743c9c6 | brimittleman | 2019-06-17 | Build site. |
| Rmd | bc3ddae | brimittleman | 2019-06-17 | add effect size nuc spec |
| html | 2b8bf0c | brimittleman | 2019-06-17 | Build site. |
| Rmd | 54946d7 | brimittleman | 2019-06-17 | add mol qtl code |
| html | 44d1fcc | brimittleman | 2019-06-16 | Build site. |
| Rmd | a5430c3 | brimittleman | 2019-06-16 | add qtl and usage analysis |
| html | 3fbf3f3 | brimittleman | 2019-06-14 | Build site. |
| Rmd | dc8d012 | brimittleman | 2019-06-14 | add nuclear specific analysis |
| html | 71ae708 | brimittleman | 2019-06-14 | Build site. |
| html | 15962c8 | brimittleman | 2019-06-14 | Build site. |
| Rmd | b38964e | brimittleman | 2019-06-14 | add pqtl overlap |
| html | 4912eaa | brimittleman | 2019-06-14 | Build site. |
| Rmd | bf91cb3 | brimittleman | 2019-06-14 | add location plot |
| html | 2c39fd1 | brimittleman | 2019-06-11 | Build site. |
| html | 9820e7e | brimittleman | 2019-06-11 | Build site. |
| Rmd | abd1ae9 | brimittleman | 2019-06-11 | add geno proc info |
| html | 5d71c2e | brimittleman | 2019-06-10 | Build site. |
| Rmd | c5fe1c2 | brimittleman | 2019-06-10 | add motif disruption |
| html | f81a440 | brimittleman | 2019-06-07 | Build site. |
| Rmd | 02d97db | brimittleman | 2019-06-07 | add intron ratio file |
| html | 458e494 | brimittleman | 2019-06-07 | Build site. |
| html | 4c50025 | brimittleman | 2019-06-06 | Build site. |
| Rmd | 8710e5c | brimittleman | 2019-06-06 | add new analysis for unex v ex |
| html | 0e20f3a | brimittleman | 2019-06-05 | Build site. |
| Rmd | c743502 | brimittleman | 2019-06-05 | first pass overlap |
| html | d30d453 | brimittleman | 2019-05-30 | Build site. |
| Rmd | 1321989 | brimittleman | 2019-05-30 | add chromhmm analysis |
| html | a71262e | brimittleman | 2019-05-29 | Build site. |
| Rmd | 6432c1b | brimittleman | 2019-05-29 | inititate nascent analysis |
| html | 28c8ca3 | brimittleman | 2019-05-24 | Build site. |
| html | a88eedf | brimittleman | 2019-05-20 | Build site. |
| Rmd | 8f883d8 | brimittleman | 2019-05-20 | add overlap analysis |
| html | d89772d | brimittleman | 2019-05-15 | Build site. |
| html | 81a3e16 | brimittleman | 2019-05-15 | Build site. |
| Rmd | f484dcd | brimittleman | 2019-05-15 | add nascent transcription plot |
| html | 35b1f6e | brimittleman | 2019-05-15 | Build site. |
| Rmd | 90e0c4d | brimittleman | 2019-05-15 | add reg heatmap |
| html | bf3a1e0 | brimittleman | 2019-05-14 | Build site. |
| Rmd | 77ca26a | brimittleman | 2019-05-14 | results by logef |
| html | 144c00b | brimittleman | 2019-05-08 | Build site. |
| Rmd | 5e39f1c | brimittleman | 2019-05-08 | choose pcs and start qtl rerun |
| html | f5af9c6 | brimittleman | 2019-05-08 | Build site. |
| Rmd | 1ba7d2b | brimittleman | 2019-05-08 | add pca |
| html | 9062ebd | brimittleman | 2019-05-03 | Build site. |
| Rmd | 0e5af55 | brimittleman | 2019-05-03 | add utr coverage |
| html | 53eeea4 | brimittleman | 2019-05-02 | Build site. |
| Rmd | 2067946 | brimittleman | 2019-05-02 | add old vs new data usage analysis |
| html | 60093ce | brimittleman | 2019-05-02 | Build site. |
| Rmd | 24c2ceb | brimittleman | 2019-05-02 | add diff iso |
| html | ac656aa | brimittleman | 2019-04-30 | Build site. |
| Rmd | f9b8195 | brimittleman | 2019-04-30 | understand usage of new pas |
| html | e3bdc3a | brimittleman | 2019-04-29 | Build site. |
| html | be227e7 | brimittleman | 2019-04-25 | Build site. |
| html | b2525c3 | brimittleman | 2019-04-24 | Build site. |
| Rmd | 9bbe437 | brimittleman | 2019-04-24 | add corr analysis |
| html | 214c05c | brimittleman | 2019-04-23 | Build site. |
| Rmd | 27b11e3 | brimittleman | 2019-04-23 | start signal site analysis |
| html | 1fb7086 | brimittleman | 2019-04-23 | Build site. |
| html | e650e08 | brimittleman | 2019-04-22 | Build site. |
| Rmd | 851c963 | brimittleman | 2019-04-22 | add reads against feature |
| html | 28bd046 | brimittleman | 2019-04-18 | Build site. |
| Rmd | 017f5c0 | brimittleman | 2019-04-18 | add map apa qtl pipeline |
| html | 874081d | brimittleman | 2019-04-18 | Build site. |
| Rmd | 22bfb66 | brimittleman | 2019-04-18 | add pas usage qc analysis |
| html | aab1fca | brimittleman | 2019-04-17 | Build site. |
| Rmd | 057dc1a | brimittleman | 2019-04-17 | add bam 2 pas analysis |
| html | fd1f8cb | brimittleman | 2019-04-13 | Build site. |
| Rmd | f5e23f3 | brimittleman | 2019-04-11 | add fastq 2 bam |
| html | 444f1c7 | brimittleman | 2019-04-11 | Build site. |
| html | 1c955c5 | brimittleman | 2019-04-11 | Build site. |
| Rmd | 0f343f8 | brimittleman | 2019-04-11 | Start workflowr project. |
Welcome to my research website.
In the preprocessing steps of the analysis I will go from the fastq files that come off the sequencer to the PAS I will use for the rest of the analysis.
These files create some of the QC metrics I used for the analysis.