Last updated: 2020-02-11

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Knit directory: apaQTL/analysis/

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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/run_qtlFacetBoxplots.sh
    Deleted:    code/test.txt
    Deleted:    reads_graphs.Rmd

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Rmd f9b8195 brimittleman 2019-04-30 understand usage of new pas
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Rmd 39a6572 brimittleman 2019-04-29 add correlation genotype heatmap
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Rmd 549c7ff brimittleman 2019-04-12 add helper scripts for pas snake
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Rmd f5e23f3 brimittleman 2019-04-11 add fastq 2 bam
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Rmd 0f343f8 brimittleman 2019-04-11 Start workflowr project.

Welcome to my research website.

Preprocessing:

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.

QC and base visualization:

These files create some of the QC metrics I used for the analysis.

apaQTL

Differential Isoform Analysis

Characterize apaQTLs and compare to eQTLs

Graph from Mayher

Additional QC about MP

Exploratory analysis not used in MS

Revisions (Thank you to the reviewers for suggestions)