Last updated: 2018-08-17

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    File Version Author Date Message
    Rmd 392aed9 brimittleman 2018-08-17 lift code and add to index

I will use this analysis to create a pipeline I can use to liftover the peaks once I get them from the human and chimp three prime seq data.

Download files

Tool to add to conda environment:

  • ucsc-liftover

Chain file from UCSC:

  • /project2/gilad/briana/genome_anotation_data/comp_genomes/liftover/hg38ToPanTro5.over.chain.gz

  • /project2/gilad/briana/genome_anotation_data/comp_genomes/liftover/panTro5ToHg38.over.chain.gz

Prepare the bed files

I want the bed files with the peaks to be in the folowing format:

chr# start end species_peakname

Resulting bed files will go in: /project2/gilad/briana/comparitive_threeprime/data/liftover

To go from the peak bed file created in the callPeaksbySpecies analysis I need to cut the file to the first four columns and add the species name to the peak.

awk '{print $1 "\t" $2 "\t" $3 "\t" "human_"$4}' /project2/gilad/briana/comparitive_threeprime/human/data/mergedPeaks_comb/filtered_APApeaks_merged_allchrom_named_human.bed > /project2/gilad/briana/comparitive_threeprime/data/liftover/filtered_humanPeaks.bed
awk '{print $1 "\t" $2 "\t" $3 "\t" "chimp_"$4}' /project2/gilad/briana/comparitive_threeprime/chimp/data/mergedPeaks_comb/filtered_APApeaks_merged_allchrom_named_chimp.bed > /project2/gilad/briana/comparitive_threeprime/data/liftover/filtered_chimpPeaks.bed

Run liftover

Run liftOver with ‘liftOver input.bed hg18ToHg19.over.chain.gz output.bed unlifted.bed’ I want to run it both direction. I will then lift back.

LiftForward.sh

#!/bin/bash

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

module load Anaconda3
source activate comp_threeprime_env

#human to chimp
liftOver /project2/gilad/briana/comparitive_threeprime/data/liftover/filtered_humanPeaks.bed /project2/gilad/briana/genome_anotation_data/comp_genomes/liftover/hg38ToPanTro5.over.chain.gz /project2/gilad/briana/comparitive_threeprime/data/liftover/filtered_humanPeakslifted.bed /project2/gilad/briana/comparitive_threeprime/data/liftover/filtered_humanPeaksunlifted.bed
 

#chimp to human 
liftOver /project2/gilad/briana/comparitive_threeprime/data/liftover/filtered_chimpPeaks.bed /project2/gilad/briana/genome_anotation_data/comp_genomes/liftover/panTro5ToHg38.over.chain.gz /project2/gilad/briana/comparitive_threeprime/data/liftover/filtered_chimpPeaks.lifted.bed /project2/gilad/briana/comparitive_threeprime/data/liftover/filtered_chimpPeaks.unlifted.bed

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

This reproducible R Markdown analysis was created with workflowr 1.1.1