Last updated: 2020-01-27

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Knit directory: Comparative_APA/analysis/

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Unstaged changes:
    Modified:   analysis/ExploredAPA.Rmd
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    Modified:   analysis/comp2apaQTLPAS.Rmd
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    Modified:   analysis/speciesSpecific.Rmd
    Modified:   analysis/speciesSpecific_DF.Rmd

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Rmd 4ed237b brimittleman 2020-01-27 add code for expression plots
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Rmd a255e22 brimittleman 2019-10-16 add code and annotations for dt plots

I created merged Bam files in the snakefiles. I will create bigwigs with all of these.

  • ../Human/data/mergedbyFracBam/human_Nuclear.SamplesMerged.sort.bam

  • ../Human/data/mergedbyFracBam/human_Total.SamplesMerged.sort.bam

  • ../Chimp/data/mergedbyFracBam/chimp_Nuclear.SamplesMerged.sort.bam

  • ../Chimp/data/mergedbyFracBam/chimp_Total.SamplesMerged.sort.bam

mkdir ../Chimp/data/mergedbw_byFrac/
mkdir  ../Human/data/mergedbw_byFrac/

sbatch mergedBam2BW.sh
mkdir ../data/DTmatrix/
mkdir ../output/dtPlots/
sbatch transcriptDTplotsNuclear.sh

sbatch transcriptDTplotsTotal.sh

Do this for expression as well.

First I will merge RNA and create BW for the expression RNA seq data.

mkdir ../Human/data/RNAseq/mergeBam
mkdir ../Human/data/RNAseq/mergeBW

mkdir ../Chimp/data/RNAseq/mergeBam
mkdir ../Chimp/data/RNAseq/mergeBW

sbatch mergeandBWRNAseq.sh

sbatch RNATranscriptDTplot.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_1.5.0 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