Smoothing a bedgraph file¶
usage: smooth_bedgraph.py [-h] [-j JID] -f INPUT_LIST [-w WINDOW_SIZE]
[-s STEP_SIZE] [-g GENOME] [-cs CHROM_SIZE]
Smooth bedgraph
optional arguments:
-h, --help show this help message and exit
-j JID, --jid JID enter a job ID, which is used to make a new directory.
Every output will be moved into this folder. (default:
smooth_bedgraph_yli11_2021-06-29)
-f INPUT_LIST, --input_list INPUT_LIST
a list of bedgraph files (default: None)
-w WINDOW_SIZE, --window_size WINDOW_SIZE
window size (default: 200)
-s STEP_SIZE, --step_size STEP_SIZE
step size (default: 20)
Genome Info:
-g GENOME, --genome GENOME
genome version: hg19, hg38, mm9, mm10. By default,
specifying a genome version will automatically update
index file, black list, chrom size and
effectiveGenomeSize, unless a user explicitly sets
those options. (default: hg19)
-cs CHROM_SIZE, --chrom_size CHROM_SIZE
chrome size (default: /home/yli11/Data/Human/hg19/anno
tations/hg19.chrom.sizes)
Summary¶
This tool will smooth a bedgraph file given a window size and step size using bedops
. Main command behind this tool is:
bedops -w $window_size --stagger $step_size --range $window_size $$.temp.ref | bedmap --skip-unmapped --faster --echo --mean --delim "\t" --bases-uniq-f - $$.temp.ref | awk -F "\t" '{print ($1"\t"$2"\t"$2+1"\t"$4*$5)}' > $(basename ${COL1}).smooth.bdg
Using -w
and -s
to control smoothness. Basically, the higher w/s
ratio, the more smoothed output it will be.
Usage¶
Copy and paste all bedgraph files (e.g., *.bdg or *bedgraph or *wig) into your working directory, and:
hpcf_interactive
module load python/2.7.13
ls * > input.list
smooth_bedgraph.py -f input.list -g hg19
Output¶
Smoothed bw file will be stored in the {{jid}} folder.
Comments¶
code @ github.