List Everything we tried to fix dominance problem

Last updated: 2020-04-02

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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
    Modified:   analysis/SpliceSiteStrength.Rmd
    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/speciesSpecific.Rmd
    Modified:   analysis/upsetter_DF.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File	Version	Author	Date	Message
Rmd	725ee54	brimittleman	2020-04-02	add test for overlap
html	3b7192e	brimittleman	2020-04-02	Build site.
Rmd	788b72c	brimittleman	2020-04-02	add list of problems

I will use this file to list everything that I did to try to fix the different location for dominance problem.

Various cutoffs for level of dominance:

10%
20%
30%
40%
50%
Checked that dominance is not driven by counts at 30%

Remove all reads with N’s
Change misprime filter:

60% T’s in 10 bases upstream
50% T’s in 10 bases upstream (flips distribution)
40% T’s in 10 basesupstream (flips distribution)

Multimapping variation:

Inclue primary reads
Remove PAS most effected by multimapping (top 2%)
Remove genes with PAS most effected

Ways to call dominance:

Different dominant PAS in different locations
Remove genes with ties in dominant PAS
Remove genes with 1 PAS

Normalization Methods:

Quantile normalize
Leafcutter normalization (flips distribution)

Orthologous exons:

Remove genes without at least 1 orthologous exon

Test to seperate read quality:

MAPQ scores
Mismatch
Star alignment scores

Tests for annotation bias:

intronic location with human annotation
intronic PAS upstream distance of ortho exon
intronic PAS downstream distance of ortho exon
intronic PAS proportion of distance between ortho exons

Remove PAS that overlap

sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] workflowr_1.6.0 Rcpp_1.0.2      digest_0.6.18   later_0.7.5    
 [5] rprojroot_1.3-2 R6_2.3.0        backports_1.1.2 git2r_0.26.1   
 [9] magrittr_1.5    evaluate_0.12   stringi_1.2.4   fs_1.3.1       
[13] promises_1.0.1  whisker_0.3-2   rmarkdown_1.10  tools_3.5.1    
[17] stringr_1.3.1   glue_1.3.0      httpuv_1.4.5    yaml_2.2.0     
[21] compiler_3.5.1  htmltools_0.3.6 knitr_1.20

List Everything we tried to fix dominance problem

Briana Mittleman

4/2/2020