Last updated: 2019-02-19

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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/NewPeakPostMP.Rmd
    Modified:   analysis/apaQTLoverlapGWAS.Rmd
    Modified:   analysis/characterize_apaQTLs.Rmd
    Modified:   analysis/cleanupdtseq.internalpriming.Rmd
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    Modified:   analysis/dif.iso.usage.leafcutter.Rmd
    Modified:   analysis/diffIsoAnalysisNewMapping.Rmd
    Modified:   analysis/diff_iso_pipeline.Rmd
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    Modified:   analysis/explore.filters.Rmd
    Modified:   analysis/flash2mash.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:   code/Snakefile

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Rmd 6aa94e4 Briana Mittleman 2019-01-16 plots for 5% usage
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Rmd 413c8fd Briana Mittleman 2018-11-29 add filter QTL analysis and start explain pqtl
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Rmd a9d3372 Briana Mittleman 2018-11-15 fix gwas bullet
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Rmd b5f744f Briana Mittleman 2018-11-06 initiate flash2mash
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Rmd 96a97f4 Briana Mittleman 2018-10-24 add nuclear characterization
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Rmd c8dbaf0 Briana Mittleman 2018-10-22 add apa prot rna overlap
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Rmd f819c8e Briana Mittleman 2018-10-11 add distance metric analsis total apaQTL
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Rmd eda266e Briana Mittleman 2018-09-26 test peak to gene transcript dist
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Rmd 46b7343 Briana Mittleman 2018-09-06 add overlap analysis with code to subset
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Rmd 2d41f11 Briana Mittleman 2018-07-25 add expand smash to index
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Rmd 4fede84 Briana Mittleman 2018-07-16 add eval brain analysis
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Rmd 4a84769 Briana Mittleman 2018-07-13 add analysis for coparing coverage of RNAseq and 3’ seq
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Rmd 8b622c3 Briana Mittleman 2018-07-05 add denovo to index
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Rmd 642faf0 Briana Mittleman 2018-06-13 start PAS enrichment analysis
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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 https://brimittleman.github.io/Net-seq/

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