PAS descriptive plots

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Ignored files:
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    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    output/.DS_Store

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    Untracked:  code/._callPeaksYL.py
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Unstaged changes:
    Modified:   README.md
    Modified:   analysis/._fastq2bam.Rmd
    Modified:   analysis/PASusageQC.Rmd
    Modified:   analysis/Readdistagainstfeatures.Rmd
    Modified:   analysis/_site.yml
    Modified:   analysis/about.Rmd
    Modified:   analysis/bam2pas.Rmd
    Modified:   analysis/license.Rmd
    Modified:   analysis/mapapaQTL.Rmd
    Modified:   code/Snakefile
    Modified:   code/SnakefilePAS
    Modified:   code/SnakefilefiltPAS
    Modified:   code/UsageDifferenceHeatmap.R
    Modified:   code/apaQTLCorrectPvalMakeQQ.R
    Modified:   code/apaQTL_Nominal.sh
    Modified:   code/apaQTL_permuted.sh
    Modified:   code/apaQTLsnake.err
    Modified:   code/apaQTLsnake.out
    Modified:   code/bed2saf.py
    Modified:   code/callPeaksYL.py
    Modified:   code/chooseAnno2SAF.py
    Modified:   code/cluster.json
    Modified:   code/clusterPAS.json
    Modified:   code/clusterfiltPAS.json
    Modified:   code/config.yaml
    Modified:   code/convertNumeric.py
    Modified:   code/filter5perc.R
    Modified:   code/filter5percPheno.py
    Modified:   code/filterpeaks.py
    Modified:   code/fixFChead.py
    Modified:   code/make5percPeakbed.py
    Modified:   code/makeFileID.py
    Modified:   code/makePheno.py
    Modified:   code/makeSampleList.py
    Modified:   code/mergeAllBam.sh
    Modified:   code/mergeByFracBam.sh
    Modified:   code/mergePeaks.sh
    Modified:   code/namePeaks.py
    Modified:   code/peak2PAS.py
    Modified:   code/peakFC.sh
    Modified:   code/pheno2countonly.R
    Modified:   code/quantassign2parsedpeak.py
    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
    Modified:   code/test.txt
    Modified:   data/MetaDataSequencing.txt
    Modified:   output/README.md

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