[BioC] NucleR: processReads/solveUserSEW0 - Error

Oscar Flores oflores at mmb.pcb.ub.es
Thu Nov 3 13:16:39 CET 2011

Hi Stefanie,

I'm the developer of nucleR, so let's see if I can help you ;)

After the processing, processReads converts the input data to a RangedData
object for a easier manipulation later, so this error is occurs at the last
step of the call, but data can be messed in previous steps. It's 
hard to tell what is happening without having a look to the input data,
which I guess is huge...

I would like to have a look to the raw data, but I know it is difficult
to send it if it's not in a public repository. Maybe you can contact me
directly about that (oflores at mmb.pcb.ub.es)...

Meanwhile, if you want to try a workaround, you can directly convert the 
imported reads to RangedData format (which is the other format supported
by processReads):

(being "ar" your imported AlignedReads object)

res = RangedData(IRanges(start=position(ar),width=width(ar)),
strand=strand(ar),space=ar at chromosome)

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

This should work, but will be nice to have a look to your data
to fix a possible problem in the AlignedReads method.



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