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.
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
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