Last updated: 2017-11-30

Code version: 35b1aa1

Bash script

Split genome into 200bp windows and run the coverage command:

/project2/gilad/briana/Net-seq/genome_bed/hg19_200bp_window.bed

/project2/gilad/briana/Net-seq/ref_genes/windows_200

make window_200_cov.sh

#!/bin/bash

#SBATCH --job-name=window_200_cov
#SBATCH --time=8:00:00
#SBATCH --partition=broadwl
#SBATCH --mem=50G
#SBATCH --tasks-per-node=4
#SBATCH --mail-type=END



bedtools coverage -counts -a /project2/gilad/briana/Net-seq/genome_bed/hg19_200bp_window.bed -b /project2/gilad/briana/Net-seq/Net-seq1/data/bed_sort/net1_18486_dep_chr_sort.bed  > /project2/gilad/briana/Net-seq/ref_genes/windows_200/window_200_cov_18486.txt


bedtools coverage -counts -a /project2/gilad/briana/Net-seq/genome_bed/hg19_200bp_window.bed -b /project2/gilad/briana/Net-seq/Net-seq1/data/bed_sort/net1_18508_dep_chr_sort.bed  > /project2/gilad/briana/Net-seq/ref_genes/windows_200/window_200_cov_18508_dep.txt

bedtools coverage -counts -a /project2/gilad/briana/Net-seq/genome_bed/hg19_200bp_window.bed -b /project2/gilad/briana/Net-seq/Net-seq1/data/bed_sort/net1_18508_nondep_chr_sort.bed   > /project2/gilad/briana/Net-seq/ref_genes/windows_200/window_200_cov_18508_nondep.txt

bedtools coverage -counts -a /project2/gilad/briana/Net-seq/genome_bed/hg19_200bp_window.bed -b /project2/gilad/briana/Net-seq/Net-seq1/data/bed_sort/net1_19238_dep_chr_sort.bed   > /project2/gilad/briana/Net-seq/ref_genes/windows_200/window_200_cov_19238.txt

bedtools coverage -counts -a /project2/gilad/briana/Net-seq/genome_bed/hg19_200bp_window.bed  -b /project2/gilad/briana/Net-seq/data/bed_sort/mayer_SRR1575922_chr_sort.bed   > /project2/gilad/briana/Net-seq/ref_genes/windows_200/window_200_cov_mayer.txt 


bedtools coverage -counts -a /project2/gilad/briana/Net-seq/genome_bed/hg19_200bp_window.bed   -b /project2/gilad/briana/Net-seq/Net-seq1/data/bed/merged_Net1.chr.bed   > /project2/gilad/briana/Net-seq/ref_genes/windows_200/window_200_cov_merged.txt

Import data

Plot data

Session information

sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] compiler_3.4.2  backports_1.1.1 magrittr_1.5    rprojroot_1.2  
 [5] tools_3.4.2     htmltools_0.3.6 yaml_2.1.14     Rcpp_0.12.13   
 [9] stringi_1.1.5   rmarkdown_1.6   knitr_1.17      git2r_0.19.0   
[13] stringr_1.2.0   digest_0.6.12   evaluate_0.10.1

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