help mapping BS treated illumina reads using rmapbs

[shawpa]

I recently ran some WGBS treated DNA on a hiseq2000 and I am trying to align it using the rmapbs software that I saw people using in the forums. Warning:I am a benchwork scientist with not much programming experience, but I am trying to learn. My question is about specifying the reference chromosome directories and the BS reads that I sequenced.

1. For specifying the chromosome directory (-c), can I point it to a folder containing all my chromosome.fa files?

2. To specify what reads I want it to analyze, can I also point it to a folder containing fastq files or does the path have to end in a specific .fastq file. Just as an FYI, illumina puts reads in separate files (I guess for data management purposes) automatically, so I have like 266 .fastq gzipped files. This might also be a problem.

Basically I am getting an error and I think these might be the source but I am not sure. I will paste the code I was running below. I probably did something stupid. I have read the manual but haven't figured out what the problem is.

/usr/local/bin/rmap/rmapbs -o /111123_SN874_0071_AD0F4CACXX/22647_aligned -c /UCSC/hg19/Sequence/Chromosomes/ /111123_SN874_0071_AD0F4CACXX/unaligned/Project_kinome_WGBS/Sample_22647_BS/read_1/

Any advice would be greatly appreciated!