Last updated: 2018-08-17

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    File Version Author Date Message
    Rmd 89d6424 brimittleman 2018-08-17 start peak calling human

Human Peaks

First I will call peaks in the merged human data like I did in https://brimittleman.github.io/threeprimeseq/peak.cov.pipeline.html

  • Merge BW
#!/bin/bash

#SBATCH --job-name=mergeBW_H
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=mergeBW_H.out
#SBATCH --error=mergeBW_H.err
#SBATCH --partition=broadwl
#SBATCH --mem=40G
#SBATCH --mail-type=END

module load Anaconda3
source activate comp_threeprime_env

ls -d -1 /project2/gilad/briana/comparitive_threeprime/human/data/bigwig/* | tail -n +2 > /project2/gilad/briana/comparitive_threeprime/human/data/list_bw/list_of_bigwig.txt

bigWigMerge -inList /project2/gilad/briana/comparitive_threeprime/human/data/list_bw/list_of_bigwig.txt /project2/gilad/briana/comparitive_threeprime/human/data/mergedBW/merged_human-threeprimeseq.bg
  • Convert to coverage

Copy the bg_to_cov.py to the code directory then run it with. ERROR HERE!

#!/bin/bash

#SBATCH --job-name=run_bgtocov_H
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=run_bgtocov_H.out
#SBATCH --error=run_bgtocov_H.err
#SBATCH --partition=broadwl
#SBATCH --mem=12G
#SBATCH --mail-type=END

module load python  

python bg_to_cov.py /project2/gilad/briana/comparitive_threeprime/human/data/mergedBW/merged_human-threeprimeseq.bg /project2/gilad/briana/comparitive_threeprime/human/data/mergedBW/merged_human-threeprimeseq.coverage.txt

  • sort -k1,1 -k2,2n /project2/gilad/briana/comparitive_threeprime/human/data/mergedBW/merged_human-threeprimeseq.coverage.txt > /project2/gilad/briana/comparitive_threeprime/human/data/mergedBW/merged_human-threeprimeseq.coverage.sort.txt

  • Call Peaks

Session information

sessionInfo()
R version 3.5.1 (2018-07-02)
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/3.5/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_1.1.1   Rcpp_0.12.18      digest_0.6.15    
 [4] rprojroot_1.3-2   R.methodsS3_1.7.1 backports_1.1.2  
 [7] git2r_0.23.0      magrittr_1.5      evaluate_0.11    
[10] stringi_1.2.4     whisker_0.3-2     R.oo_1.22.0      
[13] R.utils_2.6.0     rmarkdown_1.10    tools_3.5.1      
[16] stringr_1.3.1     yaml_2.1.19       compiler_3.5.1   
[19] htmltools_0.3.6   knitr_1.20

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