Hi everybody,

first at all: I'm quite new to R and Bioconductor (and the whole field 
of Bio-Informatics).

I'm trying to get some nuclesome positioning/peak calling data for 
further analyses. Therefor I tried the NucleR package.
The underlying data (solexa reads groomed into sanger reads) is mapped 
with Bowtie and results in a SAM-file. I converted that file to BAM 
because BAM-files can be imported with ShortRead into a format, that 
NucleR can handle.

alignedReads <- readAligned(dir, pattern=filename, type="BAM")

The imports seems to run without errors. My script (I'm using a file 
containing the R script, started from command line with R --slave 
--vanilla --file=<R-File> --args <inputfile> <more arguments> 
<outputfile>) stops at this line:

reads_pair = processReads(nucleosome_htseq, type="paired", 
fragmentLen=fragment_len)

with the following error:
/
Fehler in solveUserSEW0(start = start, end = end, width = width) :
   solving row 16512893: range cannot be determined from the supplied 
arguments (too many NAs)
Calls: processReads ... RangedData -> is -> IRanges -> solveUserSEW0 -> 
.Call/

fragmentLen is 200 in my example.
The problem is, that it's impossible to view row /16512893. /I read both 
help texts for processReads and solveUserSWE0, but I think I do not knew 
enough that it will help me much. So, maybe someone can give me a hint 
to the right way or has any idea what maybe wrong...

Thanks in advance!

Regards,
Steffi

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