[Bioc-sig-seq] Reducing Solexa's export.txt in preparation for a ChIP-seq analysis.

[ig2ar-saf2 at yahoo.co.uk]

Hello,

In preparation to analyse my own ChIP-seq data, I am trying to follow the steps described in this sample workflow:

http://www.bioconductor.org/workshops/2008/SeattleNov08/ChIP-seq/workflow.pdf

The document starts by loading data that has been "reduced to a set of alignment start positions (including orientation)".

Can somebody elaborate on that a little bit or, ideally, show it with one example?

Also, as part of the reduction, the procedure "removed all duplicate reads and applied a quality score cutoff". The score cutoff is fine but how is removing duplicates justified?

Thank you,

Ivan