Last updated: 2019-04-25

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Knit directory: threeprimeseq/analysis/

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Unstaged changes:
    Modified:   analysis/28ind.peak.explore.Rmd
    Modified:   analysis/CompareLianoglouData.Rmd
    Modified:   analysis/ExampleQTLPlot2.Rmd
    Modified:   analysis/HistoneModandPAS.Rmd
    Modified:   analysis/IndPeakUsageDiff.Rmd
    Modified:   analysis/NewPeakPostMP.Rmd
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    Modified:   analysis/RNAdecayAndAPA.Rmd
    Modified:   analysis/apaQTLoverlapGWAS.Rmd
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    Modified:   analysis/cleanupdtseq.internalpriming.Rmd
    Modified:   analysis/coloc_apaQTLs_protQTLs.Rmd
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    Modified:   analysis/diffIsoAnalysisNewMapping.Rmd
    Modified:   analysis/diff_iso_pipeline.Rmd
    Modified:   analysis/exampleQTLfacetboxplot.Rmd
    Modified:   analysis/explainpQTLs.Rmd
    Modified:   analysis/explore.filters.Rmd
    Modified:   analysis/fixBWChromNames.Rmd
    Modified:   analysis/flash2mash.Rmd
    Modified:   analysis/initialPacBioQuant.Rmd
    Modified:   analysis/mispriming_approach.Rmd
    Modified:   analysis/overlapMolQTL.Rmd
    Modified:   analysis/overlapMolQTL.opposite.Rmd
    Modified:   analysis/overlap_qtls.Rmd
    Modified:   analysis/peakOverlap_oppstrand.Rmd
    Modified:   analysis/peakQCPPlots.Rmd
    Modified:   analysis/peakQCplotsSTARprocessing.Rmd
    Modified:   analysis/pheno.leaf.comb.Rmd
    Modified:   analysis/pipeline_55Ind.Rmd
    Modified:   analysis/swarmPlots_QTLs.Rmd
    Modified:   analysis/test.max2.Rmd
    Modified:   analysis/test.smash.Rmd
    Modified:   analysis/understandPeaks.Rmd
    Modified:   analysis/unexplainedeQTL_analysis.Rmd
    Modified:   code/Snakefile

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Rmd 539892a Briana Mittleman 2018-05-01 Start workflowr project.

Briana Mittleman

This is the site I will use for my human 3’ seq project. I will have my workflow and analysis here. The three prime seq protocol I am using is Lexogen, QuantSeq 3’ mRNA-Seq library kit. The first analysis will be on the total and nucleic fractions of the LCL used in the net-seq analysis found at

Initial analysis on RNA seq of nuclear and total fractions:

Explore and filter mis-primming:

Peak calling:

Rerun analysis opp strand:

Evaluate and learn from QTLs:

Analysis for all 39 indivduals:

Data analysis post MP cleaning and filtering

In the previous sections (specifically here) I reran some QC and the QTL analysis with the filtered and clean data. Here I want to look at some of the other analysis with the processed data.

55 Individuals

I now have 55 individuals. I am going to call peaks and QTLs in this data.

New processing pipeline - STAR with WASP

Reprocess after resequencing

After resequencing I am going to start using a new data folder to differentiate the new processing. This will be data_reseq. I will also create a new snakefile for the new pipeline.