Thanks for providing the example lines. Your sam file looks nice and it should work well with my perl script to process PET data. I attached the perl script to process PET data here.
> perl process_readfiles_PET.pl [infile] [outdir] [format] [binsize] N N NULL
[infile]: name of aligned read file
[outdir]: directory that the bin-level file is exported to
[format]: format of aligned read file; either 'eland_result' or 'sam'
[binsize]: bin size
> perl process_readfiles_PET.pl example.sam . sam 150 N N NULL
Then, using the bin-level file obtained from this perl script, you can analyze your data using the following command lines:
> bin <- readBins( type = c("chip","input"), fileName=c("chip.txt_bin150.txt","input.txt_bin150.txt") )
> fit <- mosaicsFit( bin )
> peak <- mosaicsPeak( fit )
> export( peak, type="bed", filename="peak.bed" )
Please just let me know if you have any questions.