template length graph

tlengraph.R

#!/usr/bin/env Rscript


# usage:
# samtools view your_file.bam | cut -f3,4,9 > pre_bedgraph.txt
# tlengraph pre_bedgraph.txt output.bg
# bedGraphToBigWig output.bg chrom.sizes output.bw


library("ggplot2")
library("data.table")

#disable scientific notition in write.table
options(scipen=999)


args<-commandArgs(TRUE)

# use data.table to read file (format: chr, start pos, template length)
DT<-fread(args[1])

# take abs() of template length
DT$V3=abs(DT$V3)

# make bigwig spikes of length 1
DT2=data.table(DT$V1,DT$V2,DT$V2+1,DT$V3)

# sort by chr and start pos
setkeyv(DT2,c("V1","V2"))

# only take unique values
DT3=unique(DT2, by=c("V1", "V2"))

# write bedgraph
write.table(DT3,args[2],sep="\t",row.names=F,col.names=F,quote=F)