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Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    ._.DS_Store
    Ignored:    analysis/.RData
    Ignored:    analysis/.Rhistory
    Ignored:    analysis/20220707_TitrationSeries_DE_testing.nb.html
    Ignored:    code/.DS_Store
    Ignored:    code/._.DS_Store
    Ignored:    code/._DOCK7.pdf
    Ignored:    code/._DOCK7_DMSO1.pdf
    Ignored:    code/._DOCK7_SM2_1.pdf
    Ignored:    code/._FKTN_DMSO_1.pdf
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    Ignored:    code/._MAPT.pdf
    Ignored:    code/._PKD1_DMSO_1.pdf
    Ignored:    code/._PKD1_SM2_1.pdf
    Ignored:    code/.snakemake/
    Ignored:    code/5ssSeqs.tab
    Ignored:    code/Alignments/
    Ignored:    code/ChemCLIP/
    Ignored:    code/ClinVar/
    Ignored:    code/DE_testing/
    Ignored:    code/DE_tests.mat.counts.gz
    Ignored:    code/DE_tests.txt.gz
    Ignored:    code/Fastq/
    Ignored:    code/FastqFastp/
    Ignored:    code/FragLenths/
    Ignored:    code/Meme/
    Ignored:    code/Multiqc/
    Ignored:    code/OMIM/
    Ignored:    code/OldBigWigs/
    Ignored:    code/QC/
    Ignored:    code/Session.vim
    Ignored:    code/SplicingAnalysis/
    Ignored:    code/TracksSession
    Ignored:    code/bigwigs/
    Ignored:    code/featureCounts/
    Ignored:    code/geena/
    Ignored:    code/igv_session.template.xml
    Ignored:    code/igv_session.xml
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    Ignored:    data/._Hijikata_TableS1_41598_2017_8902_MOESM2_ESM.xls
    Ignored:    data/._Hijikata_TableS2_41598_2017_8902_MOESM3_ESM.xls
    Ignored:    output/._PioritizedIntronTargets.pdf

Untracked files:
    Untracked:  analysis/20220804_MakeBigwigListTsv.Rmd
    Untracked:  analysis/20220809_geena.Rmd
    Untracked:  analysis/20220822_Check_chRNA.Rmd
    Untracked:  analysis/20220907_IdentifyTargetsForVerification.Rmd
    Untracked:  code/scripts/Collapse_Juncfiles.R
    Untracked:  data/Hijikata_Table2_combined.csv
    Untracked:  data/Risdplam_Branaplam_specific_exons 5'ss.xlsx
    Untracked:  output/FibroblastOMIM_GOF_Downregulated_AndCrypticSpliced_GeneList.tsv

Unstaged changes:
    Modified:   analysis/20211216_DifferentialSplicing.Rmd
    Modified:   analysis/20220629_FirstGlanceTitrationSeries.Rmd
    Modified:   analysis/20220712_FitDoseResponseModels.Rmd
    Modified:   analysis/20220726_Check_chRNATestSeq.Rmd
    Modified:   analysis/index.Rmd
    Modified:   code/Snakefile
    Modified:   code/config/config.yaml
    Modified:   code/config/samples.chRNAPilotSequencing.tsv
    Modified:   code/rules/Process_chRNA.smk
    Modified:   code/rules/RNASeqProcessing.smk
    Modified:   code/rules/common.smk
    Modified:   code/scripts/GenometracksByGenotype
    Modified:   output/QC/ReadCountsAndJunctionsPerSamples.tsv

Staged changes:
    Modified:   .gitmodules
    New:        code/scripts/GenometracksByGenotype

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