Last updated: 2019-09-04

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Knit directory: apaQTL/analysis/

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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

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Rmd c743502 brimittleman 2019-06-05 first pass overlap
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Rmd 1321989 brimittleman 2019-05-30 add chromhmm analysis
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Rmd 77ca26a brimittleman 2019-05-14 results by logef
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Rmd 5e39f1c brimittleman 2019-05-08 choose pcs and start qtl rerun
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Rmd 1ba7d2b brimittleman 2019-05-08 add pca
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Rmd f9b8195 brimittleman 2019-04-30 understand usage of new pas
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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