Add files via upload

#!/usr/bin/Rscript

args <- commandArgs()

#print(args)

dir <- args[6]

Name <- args[7]

#tail -n +5 RNA_2500.mm10.read_distribution.txt | head -n -1 > temp2.txt

#head -n 3 RNA_2500.mm10.read_distribution.txt | grep Assigned | sed 's/Total Assigned Tags//g' | sed 's/ //g'

Df <- read.table(paste(dir,"temp1.txt",sep="/"), header = T)

Total_tag <- as.numeric(read.table(paste(dir,"temp2.txt",sep="/"), header = F)); Total_tag

Df2 <- data.frame(Df$Group,Df$Tag_count)

colnames(Df2) <- c("Group", "Tag_count")

Inter <- data.frame("Intergenic",Total_tag-sum(Df2$Tag_count[1:4]))

colnames(Inter) <- c("Group", "Tag_count")

Df3 <- rbind(Df2,Inter)

Df3$Tag_perc <- Df3$Tag_count/Total_tag*100; Df3

temp <- paste(Name,'.reads_distribution.pdf', sep="")

pdf(paste(dir,temp, sep="/"))

barplot(Df3$Tag_perc[c(1:4,11)], names.arg=Df3$Group[c(1:4,11)], cex.names = 0.9,

        ylab="Percentage of reads (%)", main="Reads distribution")

dev.off()

temp <- paste(Name,".reads_distribution2.txt", sep="")

write.table(Df3,paste(dir, temp, sep="/"), quote = F, row.names=F, sep="\t")

 No newline at end of file

[Header],,,,,

IEMFileVersion,4,,,,

Investigator Name,Travis Law,,,,

Experiment Name,ATAC-ChIP1 & ATAC-ChIP2 & ATAC-unbound1 & ATAC & ATAC-unbound2,,,,

Date,03/29/2018,,,,

Workflow,GenerateFASTQ,,,,

Application,FASTQ Only,,,,

Assay,Nextera,,,,

Description,,,,,

Chemistry,Amplicon,,,,

,,,,,

[Reads],,,,,

30,,,,,

30,,,,,

,,,,,

[Settings],,,,,

,,,,,

[Data],,,,,

Sample_ID,Sample_Name,I7_Index_ID,index,I5_Index_ID,index2

filler,filler,N701,AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA,N502,AAAAAAAA