Hi Kelly,

yes, the extend parameter is supposed to represent the estimated average
fragment size of the sonicated DNA.

Lukas



On Tue, Dec 17, 2013 at 5:26 AM, Vining, Kelly <Kelly.Vining@oregonstate.edu
> wrote:

> Hello BioC group,
> This question was already forwarded to this list (thanks Herve Pages), but
> I am also posting it to confirm that it has not yet been answered.
> I have a question about the 'extend' vs. 'shift' parameters in the MEDIPS
> package. From the documentation:
>
> "All reads will be extended to a length of 300nt according to the given
> strand information:
> extend=300
> As an alternative to the extend parameter, the shift parameter can be
> specified. Here, the reads are not extended but shifted by the specified
> number of nucleotides with respect to the given strand information. One of
> the two parameters extend or shift has to be 0."
>
> Is this extend parameter supposed to represent the IP'd fragment size?
>
> Thanks for any help,
> --Kelly V.
>
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