[BioC] Question about MEDIPS extend parameter

Vining, Kelly Kelly.Vining at oregonstate.edu
Tue Dec 17 14:26:28 CET 2013

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:
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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