[BioC] NucleR: processReads/solveUserSEW0 - Error

Oscar Flores oflores at mmb.pcb.ub.es
Wed Nov 9 15:35:00 CET 2011

El 09/11/2011 13:38, Stefanie Ververs escribió:
> I got some smaller input file and will try to use it for NucleR, too. 
> By now:

The problem you have with nucleR is in the last part of processReads, 
but seems it is not related a malfunction of nucleR but is due the 
creation of a RangedData object with <NA> values. See:

 > RangedData(IRanges(NA))
Error in solveUserSEW0(start = start, end = end, width = width) :
   solving row 1: range cannot be determined from the supplied arguments 
(too many NAs)

I don't have experience working with BAM files, but could be that you 
have an extra blank line at the end of your file and this creates a NA 
record? Which is the output of:

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

Also, FYI, if you type "options(error=recover)" you will be able to see 
the calling stack of the different functions when an error ocurres. You 
can then look at the variables in that namespace (with "ls") and take a 
look at them, maybe this could help...

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