Test SMASH

Last updated: 2018-07-17

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Untracked files:
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File	Version	Author	Date	Message
Rmd	89ebcac	Briana Mittleman	2018-07-17	add smash test

In this analysis I will use the tutorial I did for the SMASH package on chip seq data to test it on the three prime seq data. In order to complete this I need to make a matrix with genome location counts for where reads start for positions 880001:1011072 on chr1, I am using this region because I already know it fits the \(2^{x}\) criterion. I need the matrix to be individual by basepair. I can use genome cov in all of the total fractions then merge the results together to make a matrix.

#!/bin/bash

#SBATCH --job-name=5gencov
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=5gencov.out
#SBATCH --error=5gencov.err
#SBATCH --partition=broadwl
#SBATCH --mem=40G
#SBATCH --mail-type=END


module load Anaconda3
source activate three-prime-env 

#imput sorted bam file 
bam=$1

describer=$(echo ${bam} | sed -e 's/.*\YL-SP-//' | sed -e "s/-sort.bam$//")


bedtools genomecov-ibam $1 -d  -5 > /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.${describer}.bed

run on /project2/gilad/briana/threeprimeseq/data/sort/YL-SP-18486-N_S10_R1_001-sort.bam

wrap this function:

#!/bin/bash

#SBATCH --job-name=w_5gencov
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=w_5gencov.out
#SBATCH --error=w_5gencov.err
#SBATCH --partition=broadwl
#SBATCH --mem=16G
#SBATCH --mail-type=END


module load Anaconda3
source activate three-prime-env 

for i in $(ls /project2/gilad/briana/threeprimeseq/data/sort/*.bam); do
        sbatch 5primegencov.sh $i 
    done

First I will get ch1 880001:1011072 for each individual.

#!/bin/bash

#SBATCH --job-name=test.reg
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=test.reg.out
#SBATCH --error=test.reg.err
#SBATCH --partition=broadwl
#SBATCH --mem=20G
#SBATCH --mail-type=END

awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18486-T_S9_R1_001.bed  > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18486-T_S9_R1_001.testregion.bed


awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18497-T_S11_R1_001.bed   > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18497-T_S11_R1_001.testregion.bed


awk '$1 == 1 && $2 >= 880001 &5& $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18500-T_S19_R1_001.bed   > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18500-T_S19_R1_001.testregion.bed


awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18505-T_S1_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18505-T_S1_R1_001.testregion.bed

awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' gencov5prime.18508-T_S5_R1_001.bed  > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18508-T_S5_R1_001.testregion.bed


awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}'/project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18853-T_S31_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18853-T_S31_R1_001.testregion.bed



awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.18870-T_S23_R1_001.bed   > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.18870-T_S23_R1_001.testregion.bed


awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19128-T_S29_R1_001.bed  > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19128-T_S29_R1_001.testregion.bed


awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19141-T_S17_R1_001.bed  > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19141-T_S17_R1_001.testregion.bed


awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19193-T_S21_R1_001.bed  > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19193-T_S21_R1_001.testregion.bed


awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19209-T_S15_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19209-T_S15_R1_001.testregion.bed


awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19233-T_S7_R1_001.bed  > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19223-T_S7_R1_001.testregion.bed


awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19225-T_S27_R1_001.bed  > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19225-T_S27_R1_001.testregion.bed

awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19238-T_S3_R1_001.bed > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19238-T_S3_R1_001.testregion.bed

awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19239-T_S13_R1_001.bed  > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19239-T_S13_R1_001.testregion.bed


awk '$1 == 1 && $2 >= 880001 && $2 <= 1011072 {print}' /project2/gilad/briana/threeprimeseq/data/test.smash/gencov5prime.19257-T_S25_R1_001.bed  > /project2/gilad/briana/threeprimeseq/data/test.region/gencov5prime.19257-T_S25_R1_001.testregion.bed

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] workflowr_1.0.1   Rcpp_0.12.17      digest_0.6.15    
 [4] rprojroot_1.3-2   R.methodsS3_1.7.1 backports_1.1.2  
 [7] git2r_0.21.0      magrittr_1.5      evaluate_0.10.1  
[10] stringi_1.2.2     whisker_0.3-2     R.oo_1.22.0      
[13] R.utils_2.6.0     rmarkdown_1.8.5   tools_3.4.2      
[16] stringr_1.3.1     yaml_2.1.19       compiler_3.4.2   
[19] htmltools_0.3.6   knitr_1.18

This reproducible R Markdown analysis was created with workflowr 1.0.1

Test SMASH

Briana Mittleman

7/16/2018

Session information