Hi all
I have maq paired-end alignment files that I want to read into R. I have tried to browse several packages and they all seem to depend on ShortRead package of bioconductor which does not currently support paired-end reads. Does anybody know of any Bioconductor packages which support paired-end alignment data. As there are lot of good coverage plot functions in bioconductor I want to utilize them thus it would be great if some one could suggest any package that has support for paired-end alignment reading. Also I have tried to use my own scripts for plotting coverage and I want to overlay the coverage of all the chromosomes in one graph (using different colors e.t.c) It would be great to know If anybody has tried to implement it too.
Since the files are too big it takes a lot of time if I want to plot data for all the chromosomes at the same time. Following is the code that I found somewhere and have modified to my needs but it takes a lot of time if I want to plot the data for all chromosomes. Following is the code I use it for a single chromosome I am wondering how can I plot the data for all the chromosomes in one plot and more efficiently.
data <-read.table(file="croppedpileup.out",sep="\t",header=F)
colnames(data)<-c("pos","consensus","coverage")
depth<-mean(data[,"coverage"])
# depth now has the mean (overall)coverage
#set the bin-size
window<-101
rangefrom<-0
rangeto<-length(data[,"pos"])
data.smoothed<-runmed(data[,"coverage"],k=window)
png(file="cov_out.png",width=1900,height=1000)
plot(x=data[rangefrom:rangeto,"pos"],y=data.smoothed[rangefrom:rangeto],pch=".", cex=1,xlab="bp position",ylab="depth",type="l")
dev.off()
Thanks
