New Deep tools plots

Last updated: 2019-09-26

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Knit directory: apaQTL/analysis/

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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	aa30fa2	brimittleman	2019-09-26	add new dt plots analysis

I want to make new deeptools plots for figure 1a with 5 individuals in each.

I need to merge bam files then convert to BW.

mkdir ../data/FiveMergedBam/
sbatch merge5RNAbam.sh 
sbatch merge53prime.sh

Next I need to make bigwigs for each of these:

mkdir ../data/FiveMergedBW
sbatch bam2bw.sh ../data/FiveMergedBam/RNAeuvadisBams_5mergeds.sort.bam ../data/FiveMergedBW/RNAeuvadisBams_5mergeds.sort.bw

sbatch bam2bw.sh ../data/FiveMergedBam/threeprimeN_Bams_5mergeds.sort.bam ../data/FiveMergedBam/threeprimeN_Bams_5mergeds.sort.bw

sbatch NuclearandRNA5samp_dtplots.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

New Deep tools plots

Briana Mittleman

9/25/2019