Last updated: 2019-10-07

Checks: 7 0

Knit directory: Comparative_APA/analysis/

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File Version Author Date Message
Rmd da85ad8 brimittleman 2019-10-07 add code to prepare human and chimp TvN

In this anaylsis I will complete the Chimp total vs nuclear analysis. This analysis is similar to the analysis in the apaQTL project

I need the human 5% both fraction feature counts.

Thee feature counts are in ../Chimp/data/CleanLiftedPeaks_FC/ALLPAS_postLift_LocParsed_Chimp_fixed.fc. I need to subset these for those in the annotations. Keep the PAS in this file: ../data/Peaks_5perc/Peaks_5perc_either_HumanCoordHummanUsage.bed. I will do this with a python script.

mkdir ../Chimp/data/CleanLiftedPeaks4LC/
python prepareCleanLiftedFC_5perc4LC.py ../Chimp/data/CleanLiftedPeaks_FC/ALLPAS_postLift_LocParsed_Chimp_fixed.fc ../data/Peaks_5perc/Peaks_5perc_either_HumanCoordHummanUsage.bed ../Chimp/data/CleanLiftedPeaks4LC/ALLPAS_postLift_LocParsed_Chimp_fixed4LC.fc

This will only look at PAS on chromosomes 1-22 no extra haplotpyes.

mkdir ../Chimp/data/DiffIso_Chimp/

python subset_diffisopheno_Chimp_tvN.py 1
python subset_diffisopheno_Chimp_tvN.py 2
python subset_diffisopheno_Chimp_tvN.py 3
python subset_diffisopheno_Chimp_tvN.py 4
python subset_diffisopheno_Chimp_tvN.py 5
python subset_diffisopheno_Chimp_tvN.py 6
python subset_diffisopheno_Chimp_tvN.py 7
python subset_diffisopheno_Chimp_tvN.py 8
python subset_diffisopheno_Chimp_tvN.py 9
python subset_diffisopheno_Chimp_tvN.py 10
python subset_diffisopheno_Chimp_tvN.py 11
python subset_diffisopheno_Chimp_tvN.py 12
python subset_diffisopheno_Chimp_tvN.py 13
python subset_diffisopheno_Chimp_tvN.py 14
python subset_diffisopheno_Chimp_tvN.py 15
python subset_diffisopheno_Chimp_tvN.py 16
python subset_diffisopheno_Chimp_tvN.py 18
python subset_diffisopheno_Chimp_tvN.py 19
python subset_diffisopheno_Chimp_tvN.py 20
python subset_diffisopheno_Chimp_tvN.py 21
python subset_diffisopheno_Chimp_tvN.py 22

Make sample groups:

python makeSamplyGroupsChimp_TvN.py

Run Leafcutter:

sbatch runChimpDiffIso.sh

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_1.4.0 Rcpp_1.0.2      digest_0.6.18   rprojroot_1.3-2
 [5] backports_1.1.2 git2r_0.25.2    magrittr_1.5    evaluate_0.12  
 [9] stringi_1.2.4   fs_1.3.1        whisker_0.3-2   rmarkdown_1.10 
[13] tools_3.5.1     stringr_1.3.1   glue_1.3.0      yaml_2.2.0     
[17] compiler_3.5.1  htmltools_0.3.6 knitr_1.20