singleEnd = FALSE for ChIPseqSpikeInFree wrapper script

[MoniDR]

Hi,

I was wondering if you could help me clarify the processing of paired end data.
I've noticed that while you can set singleEnd =FALSE argument for the CountRawReads() function, it is not possible with the wrapper function, which then by default treats the data as single end.

I did try to run functions on their own, but it then stops at the parsing step giving the error:
ooops: you need to change metadata file **\n

Thank you for your help!

Monica

[khucnam]

I tried to modify the CountRawReads() function using the command:
trace("CountRawReads", edit=TRUE)
Then in the text editor, I changed to singleEnd =FALSE, save file, back to R and run again.

However, this return read count to 0 for all samples --> leading to the following error
WARNING Some samples were removed due to library size(< 10^6) or no read count [ n= 10 ]:
bin sample1.bam sample2.bam
Error in datOut[, -1] : incorrect number of dimensions

Still I don't know how to use it with Paired-end reads.