Hi,

I want to compare the peaks from two separate chip seq samples.

I'm trying to use MAnorm (R version) on a MacOS unix command line, but I'm having trouble.

Now the program runs through "step1" without any errors, but it doesn't seem to be making a pair of essential files: `peak1.bed` and `peak2.bed`, so all downstream steps fail.

Below, please see the head of each of my test files, and the command I ran.

If you've used this tool before, do you have any idea why I'm having problems?

Thanks very much,

```
$ head t.*
==> t.TreatedPeaks.bed <==
1    1360    3306
1    13366    13931
1    16606    16934
1    20161    21424
1    59752    60275
1    63673    64105
1    67355    67885
1    68243    68654
1    107683    109178
1    116034    117502

==> t.controlPeaks.bed <==
1    20618    21401
1    37881    38291
1    54003    54374
1    57362    59025
1    67346    67844
1    75598    76127
1    76181    76562
1    110638    111047
1    112394    112668
1    117123    117842

==> t.controlReads.bed <==
1    2    52    -
1    11    61    -
1    32    82    -
1    32    82    -
1    32    82    -
1    32    82    -
1    37    87    +
1    37    87    -
1    47    97    -
1    62    112    -

==> t.treatedReads.bed <==
1    1    51    +
1    13    63    +
1    28    78    -
1    31    81    -
1    44    94    +
1    46    96    +
1    64    114    +
1    69    119    +
1    70    120    -
1    77    127    +

$ MAnorm.sh t.TreatedPeaks.bed t.controlPeaks.bed t.treatedReads.bed t.controlReads.bed 266 275
StepI: clean input
StepII: classify common or unique peaks
Error: Unable to open file peak1.bed. Exiting.
Error: Unable to open file peak2.bed. Exiting.
Error: Unable to open file peak1.bed. Exiting.
Error: Unable to open file peak2.bed. Exiting.
StepIII: count peak read
Error: The requested file (read1.bed) could not be opened. Error message: (No such file or directory). Exiting!
```

Here is the usage section of the readme.txt that comes with the MAnorm:

> Usage:

>   I. Create a folder and place in the folder MAnorm.sh, MAnorm.r, and all 4 bed files (peak file and read file for the 2 samples under comparison) to be analyzed.

>   II. run command:   ./MAnorm.sh   sample1_peakfile[BED]     sample2_peakfile[BED]     sample1_readfile[BED]    sample2_readfile[BED]     sample1_readshift_lentgh[INT]       sample2_readshift_length[INT]                        
                                                                                                                                                                                                                  
> ExampleCommand:  

>     ./MAnorm.sh sample1_peaks.bed sample2_peaks.bed sample1_read.bed sample2_read.bed 150 150                                                                                                                    

>    The first 4 parameters should be input files in bed format with no header lines  
>    The first 2 files have ONLY 3 columns: chromosome, start, end.  
>    The next 2 files should have 4 columns: chromosome, start, end, strand (+/-)  

>    The last 2 parameters are the number of bp to be shifted for each read. These two parameters are found from MACS peak file *_peaks.xls after "# d =".
<p>If you look at the shell script, you&#39;ll see that it&#39;s expecting UCSC chromosome names (i.e., they need to start with &quot;chr&quot;). So just quickly fix that and things should work.</p>
