https://github.com/coke6162/B2_SINE_enhancers
Tip revision: 709eaa23c1c245c9485cdeeacaf73aa18811e9e7 authored by coke6162 on 24 February 2023, 19:54:18 UTC
updated to clarify Qiao vs McCann
updated to clarify Qiao vs McCann
Tip revision: 709eaa2
call_candidate_regions.sbatch
#!/bin/bash
# Script for calling candidate regions for ABC model
# 'mm10.chrom.sizes' supplied in repos
# 'mm10-blocklist.v2.bed' can be obtained through link in README
# Example usage:
# sbatch call_candidate_regions.sbatch
## General settings
#SBATCH -p short
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --time=6:00:00
#SBATCH --mem=8G
# Job name and output
#SBATCH -J candidate_regions
#SBATCH -o /Users/%u/slurmOut/slurm-%j.out
#SBATCH -e /Users/%u/slurmErr/slurm-%j.err
# Purge modules
module purge
# Load modules
module load gcc/7.1.0 bedtools/2.28.0 python/3.7.4
# Specify names of bam and peak files
pwd; hostname; date
echo $(date +"[%b %d %H:%M:%S] Setting variable to bam and peak files...")
bamFile=$(ls *IFNG*ATAC_R1*.sorted.dedup.shifted.bam)
peakFiles=$(ls *IFNG*ATAC*_peaks.narrowPeak)
# Call candidate regions
echo $(date +"[%b %d %H:%M:%S] Calling candidate regions with makeCandidateRegions.py...")
python ABC-Enhancer-Gene-Prediction-0.2.2/src/makeCandidateRegions.py \
--narrowPeak plat_BMDM_IFNG_2h_ATAC_R1_peaks.narrowPeak \
--bam plat_BMDM_IFNG_2h_ATAC_R1.sorted.dedup.bam \
--chrom_sizes mm10.chrom.sizes \
--regions_blacklist mm10-blocklist.v2.bed \
--outDir ./ \
--peakExtendFromSummit 250 \
--nStrongestPeaks 150000
echo $(date +"[%b %d %H:%M:%S] Done")