Last updated: 2020-03-30

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Knit directory: Comparative_APA/analysis/

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Unstaged changes:
    Modified:   analysis/DiffUsedIntronic.Rmd
    Modified:   analysis/ExploredAPA.Rmd
    Modified:   analysis/ExploredAPA_DF.Rmd
    Modified:   analysis/MMExpreiment.Rmd
    Modified:   analysis/OppositeMap.Rmd
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    Modified:   analysis/TotalVNuclearBothSpecies.Rmd
    Modified:   analysis/annotationInfo.Rmd
    Modified:   analysis/changeMisprimcut.Rmd
    Modified:   analysis/comp2apaQTLPAS.Rmd
    Modified:   analysis/correlationPhenos.Rmd
    Modified:   analysis/dAPAandapaQTL_DF.Rmd
    Modified:   analysis/establishCutoffs.Rmd
    Modified:   analysis/investigatePantro5.Rmd
    Modified:   analysis/multiMap.Rmd
    Modified:   analysis/multimapParameters.Rmd
    Modified:   analysis/speciesSpecific.Rmd
    Modified:   analysis/upsetter_DF.Rmd

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Rmd 1cdc21d brimittleman 2020-01-09 add initial signal site analysis
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html a41141b brimittleman 2020-01-09 Build site.
Rmd 93ced1e brimittleman 2020-01-09 peak 2 pas
html 6d9e369 brimittleman 2020-01-08 Build site.
Rmd 203eae5 brimittleman 2020-01-08 first steps for intron loc analysis
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Rmd 6e3027a brimittleman 2020-01-07 upset plots for comparisons
html 7768535 brimittleman 2020-01-07 Build site.
Rmd 670020f brimittleman 2020-01-07 add translation protien overlap
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Rmd 54015c8 brimittleman 2020-01-06 add overlap dom with dAPA
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Rmd 5e85704 brimittleman 2020-01-06 add overlap with eQTLs
html dc41b3b brimittleman 2019-12-30 Build site.
Rmd 6214ec5 brimittleman 2019-12-30 add venn diagram for diff apa
html 42a8b12 brimittleman 2019-12-30 Build site.
Rmd 385057f brimittleman 2019-12-30 fix dom PAS on index
html 0176b49 brimittleman 2019-12-30 Build site.
Rmd 5b25363 brimittleman 2019-12-30 add total and nuclear dominant PAS analysis
html 2644747 brimittleman 2019-12-27 Build site.
Rmd 4c8973d brimittleman 2019-12-27 add total human vs chimp
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Rmd d541bb5 brimittleman 2019-12-17 move extra pcas
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Rmd de41e07 brimittleman 2019-12-16 add gene comp 5v6
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Rmd 3b64d8c brimittleman 2019-12-16 add compare ortho exon
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Rmd 8068598 brimittleman 2019-12-12 meta data by species
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Rmd f04a804 brimittleman 2019-12-08 add DE vs DS analysis
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Rmd 1452408 brimittleman 2019-12-05 add investigation pantro5
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Rmd d56d98c brimittleman 2019-12-05 add opp map
html f53ab27 brimittleman 2019-11-23 Build site.
Rmd c48aedc brimittleman 2019-11-23 add multimap stat graphs
html e7cb428 brimittleman 2019-11-21 Build site.
Rmd 9fbd1fe brimittleman 2019-11-21 figure out sample swap
html 2e33ce9 brimittleman 2019-11-21 Build site.
Rmd 17d5d33 brimittleman 2019-11-21 add diff splice without 2 samples
html 40db68c brimittleman 2019-11-19 Build site.
Rmd 7c206f8 brimittleman 2019-11-19 add extra QC anaylsis
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Rmd db85b26 brimittleman 2019-11-19 add remove 2 analysis
html dc91b0a brimittleman 2019-11-11 Build site.
Rmd b5ba82e brimittleman 2019-11-11 add diff expression and diff splicing
html 066d419 brimittleman 2019-10-16 Build site.
Rmd a255e22 brimittleman 2019-10-16 add code and annotations for dt plots
html f4bcae9 brimittleman 2019-10-15 Build site.
Rmd 25a8b1e brimittleman 2019-10-15 fix name bug add number PAS analysis
html d9f241f brimittleman 2019-10-11 Build site.
Rmd 36d8ded brimittleman 2019-10-11 add correlation between ind analysis
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Rmd c4db4f0 brimittleman 2019-10-10 add non norm pca and verify bam
html b8ccfdb brimittleman 2019-10-09 Build site.
Rmd 1f06329 brimittleman 2019-10-09 add PCA by total and nuclear
html d0c98c2 brimittleman 2019-10-09 Build site.
Rmd 14a3f66 brimittleman 2019-10-09 add pca and human v chimp in nuc analysis
html c3aa529 brimittleman 2019-10-07 Build site.
Rmd da85ad8 brimittleman 2019-10-07 add code to prepare human and chimp TvN
html 4ea2576 brimittleman 2019-10-04 Build site.
Rmd 920abac brimittleman 2019-10-04 add comaprison to old PAS
html e0ac227 brimittleman 2019-10-03 Build site.
Rmd e3f0cdf brimittleman 2019-10-03 add annotation analysis
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Rmd b5a2151 brimittleman 2019-10-01 add analysis for liftover
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Rmd 7d81da8 brimittleman 2019-10-01 add map stats to site
html 7a9cf74 brimittleman 2019-09-24 Build site.
Rmd a2fe9d6 brimittleman 2019-09-24 add annotation prep anaylsis
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Rmd b6db8f3 brimittleman 2019-09-02 add project info to about and index
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Rmd f914d49 brimittleman 2019-09-02 Start workflowr project.

I am interesting in understanding differential APA between human and chimpanzees. I used 3’ Seq to identify PAS for total and nuclear frations of LCL in both species.

Preparation and QC:

Choosing cuttoffs for usage and expression level

Catalog PAS:

Differential Isoform Analysis:

From here on, I did everything double filtered:

Human v Chimp fraction differences

Quantify Phenotypes with RNA:

Intersect with outside molecular phenotypes:

Selection exploration

Mediation

From here on, I did everything double filtered:

Evaluate Reasons for inconsistant dominance structure

Annotation differences

Visualization

Extra QC and Analysis