Last updated: 2019-05-21

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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 54fb5e2 brimittleman 2019-05-21 add normalized plot code
html e650e08 brimittleman 2019-04-22 Build site.
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

Redo with Normalized RPKM

I need to create normalized bw from each bam file. I then merge by fraction and convert back to bigwig from bedgraph.

I added a rule to the first snakefile that created the normalized files. Then I run the following to merge and create the bw.

sbatch mergeBW_norm.sh

Next I create the plot with deeptools.

sbatch BothFracDTPlotGeneRegions_normalized.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:
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 [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_1.3.0 Rcpp_1.0.0      digest_0.6.18   rprojroot_1.3-2
 [5] backports_1.1.2 git2r_0.23.0    magrittr_1.5    evaluate_0.12  
 [9] stringi_1.2.4   fs_1.2.6        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