Last updated: 2019-04-22

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Knit directory: apaQTL/analysis/

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File Version Author Date Message
Rmd 851c963 brimittleman 2019-04-22 add reads against feature

In this analysis I will create the read distribution figures. These are created using deeptools. I have merged total and nuclear bam files from the read mapping pipeline. I will convert these to bigwigs in order to map the reads against features with deeptools.

Create BW files

mkdir ../data/mergedBW_byfrac
mkdir ../data/DTmatrix
mkdir ../output/dtPlots

module load Anaconda3 
source activate three-prime-env

sbatch bam2bw.sh ../data/mergedbyFracBam/Total.SamplesMerged.sort.bam ../data/mergedBW_byfrac/Total.SamplesMerged.bw sbatch bam2bw.sh ../data/mergedbyFracBam/Nuclear.SamplesMerged.sort.bam ../data/mergedBW_byfrac/Nuclear.SamplesMerged.bw

Map along gene bodies

sbatch BothFracDTPlotGeneRegions.sh


sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.1

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
 [1] workflowr_1.2.0 Rcpp_1.0.0      digest_0.6.18   rprojroot_1.3-2
 [5] backports_1.1.3 git2r_0.24.0    magrittr_1.5    evaluate_0.13  
 [9] stringi_1.3.1   fs_1.2.6        whisker_0.3-2   rmarkdown_1.11 
[13] tools_3.5.1     stringr_1.4.0   glue_1.3.0      xfun_0.5       
[17] yaml_2.2.0      compiler_3.5.1  htmltools_0.3.6 knitr_1.21