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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:  

* [Prepare annotation files for mapping ](annotationInfo.html)  

* [Mapping statistics and plots](mapStats.html)

* [Liftover PAS](liftoverPAS.html)

* [Annotated PAS and make APA phenotype](annotatePAS.html)

* [Compare identified PAS with apaQTL PAS](comp2apaQTLPAS.html)

* [PCA plot to look at variation in data](NromalizePhenos.html)
      
* [Correlation between individuals](CorrbetweenInd.html)
      
* [Verify sample identity](verifyBAM.Rmd)

* [3' Seq enrichement along gene bodies](EnrichmentEndofGenes.html)

* [Cross map and prepare Chimp 3' for Viz in IGV](CrossChimpThreePrime.html)

* [Make PAS bed for 5% peaks](fixPeak2PAS.html)


### Choosing cuttoffs for usage and expression level  

  * [Use merged 3' at gene level to look for a data quantity cutoff](expressioncutoff.html)  

  * [Establish cutoffs by subsampleing apaQTL lines](establishCutoffs.html)  
  
  * [Compare before and after cutoff](compareFilter.html)  

##Catalog PAS:

* [Number of PAS in each species](PASnumperSpecies.html)   

    * [Number of PAS in each species double filter](PASnumberSpecies_doubleFilter.html)   

* [Pressence of top 2 signal sites](signalsites.html)  

    * [Top 2 signal sites double filter](signalsites_doublefilter.html)  

* [Dominant PAS in Nuclear Fraction](dominantPAS.html)  

    * [Dominant PAS in Nuclear Fraction double filter](dominantPAS_DF.html)  

    * [Intronic location for dominant PAS](DominantPASintronLoc.html)  
      
    * [Intronic location for dominant PAS double filter](DominantPASintronLoc_DF.html)  
    
* [Species Specificity in PAS](speciesSpecific.html)  

     * [Species Specificity in PAS double filter](speciesSpecific_DF.html)  
  


##Differential Isoform Analysis:

* [Nuclear Human vs. Chimp Analysis](Nuclear_HvC.html)  

     * [Nuclear Human vs. Chimp Analysis Double filter](Nuclear_HvC_DF.html)  

* [Explore nuclear differential APA PAS and genes](ExploredAPA.html)  

     * [Explore nuclear differential APA PAS and genes Double filter](ExploredAPA_DF.html)  

* [Enrichment for differencial APA and apaQTL](dAPAandapaQTL.html)  

     * [Enrichment for differencial APA and apaQTL double filter](dAPAandapaQTL_DF.html)   

* [Visualization for all Nuclear DAPA genes](visualizePASUsage.html)  
   
     * [Visualization for all Nuclear DAPA genes double filter](visualizePASUsage_DF.html)  

From here on, I did everything double filtered:  

* [Does presence or absense of signal explain differential usage](SS_diffUsage.html)

##Quantify Phenotypes with RNA:   

* [Differential Splicing](diffSplicing.html) 

* [Differential Expression](diffExpression.html)
  
    * [Metadata by species](MetabySpecies.html)
  
    * [DE genes and eQTLs](DEandeQTls.html)
  
* [Compare DE and DS genes](DEvDS.html)

  
##Intersect with outside molecular phenotypes:

* [Download data from differential protein and ribosomes](dProtanddRibo.html)  

* [Compare to nuclear differential APA](DiffTransProtvsNuclearAPA.html)   

     * [Compare to nuclear differential APA with Double filter](DiffTransProtvsNuclearAPA_DF.html)  

* [Use UpSetR to vizualize intersections](upsetter.html)  

    * [Use UpSetR to vizualize intersections Double filter](upsetter_DF.html)  

* [Effect size correlations](correlationPhenos.html)  

    * [Effect size correlations double filter](correlationPhenos_DF.html)  

* [Compare species 5' splice site strength](SpliceSiteStrength.html)



##Mediation  

* [Normalize Nuclear Fraction](NormalizePheno_nuclear.html)  

    * [Normalize (qqnrom) Nuclear Fraction double filter](NormalizePheno_nuclear_DF.html)    

* [Normalize clusters from splicing analysis](normalizeClusters.html)

* [Mediation analysis](mediation.html)    

    * [Mediation analysis double filter](mediation_DF.html)  
    
From here on, I did everything double filtered:  
    
* [Mediation with protein](mediation_prot.html)

* [Explore more about APA expression relationship](ExploreAPAexpression.html)

* [Explore more about APA expression relationship with overlaping significant genes](ExploreAPAexpressionOverlap.html)



##Extra QC and Analysis   

### Sample switch analysis  

* [Investigate bad RNA seq samples](InvestigateBadSamples.html)  

    * [Differential splicing without bad samples](diffSplicing_removeBad.html)  
    
    * [Differential Expression without bad samples](diffExpressionRemove2.html)  
    
### Mapping problems with pantro5 and multimapping

* [Map RNA to hg19](MapRNAhg19.html)

* [Evaluate multimapping criteria](multiMap.html)

* [Map to opposite Genomes](OppositeMap.html)

* [Evaluate Pantro 5 problems](investigatePantro5.html)

From before reseq:

* [Total Fraction](NormalizePheno_total.html)  
      
* [Total Fraction- Prenormalized](NonNormPheno_total.html)
        

### Chosing between pantro files

  * [Compare pantro5 and pantro6 orthoexon](compareOrthoExon.html)
    
  * [Differential Expression with Pantro6](diffExpressionPantro6.html)
  
  * [Compare DE in pantro5 vs pantro6](DE_pantro5vspantro6.html)


### Extra comparisons or analysis: not redone after double filter

* [Human Total vs Nuclear Analysis](Human_TvN.html)  

* [Chimp Total vs Nuclear Analysis](Chimp_TvN.html)  

* [Dominant PAS in Total Fraction](dominantPAS_total.html)  

* [Total Human vs. Chimp Analysis](Total_HvC.html)  

* [Venn diagrams for genes in each differential APA set](CompHC_totalandnuclear.html)  

From the original nuclear dominant  

   * [Does signal site explain trend?](ss_sameDomdiffDom.html)  

   * [Look at Intronic Dominant with DPAU and DE](HumanIntronicDominant.html)  

* [Enrichment for differencial APA and eQTL](DapaineQTL.html)  

* [Look at dAPA and genes from Dominant PAS analysis](DominatPASandDIffAPA.html)