[BioC] NucleR: processReads/solveUserSEW0 - Error

[Stefanie Ververs]

Hi Oscar,

thanks for your quick answer  - I think I would have contacted you, if 
there were no answers on the bioconductor-mailinglist.

I just tried the workaround as you suggested, but I got the same error 
again:
Fehler in solveUserSEW0(start = start, end = end, width = width) :
   solving row 16512893: range cannot be determined from the supplied 
arguments (too many NAs)
Calls: RangedData -> is -> IRanges -> solveUserSEW0 -> .Call

I'll think about how to show you the data (it's hosted  and processed 
with Galaxy, so it might be possible to share it.)

Regards,

Steffi

On 03.11.2011 13:16, Oscar Flores wrote:
> 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.
>
> Regards,
>
> Oscar
>
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