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

[João Fadista]

Hi,

Removing duplicates is a step that you can do in order to minimize the possible bias due to the amplification in sample preparation. 

Best,
João

-----Original Message-----
From: bioc-sig-sequencing-bounces at r-project.org [mailto:bioc-sig-sequencing-bounces at r-project.org] On Behalf Of ig2ar-saf2 at yahoo.co.uk
Sent: Thursday, March 19, 2009 3:24 PM
To: bioc-sig-sequencing at r-project.org
Subject: [Bioc-sig-seq] Reducing Solexa's export.txt in preparation for aChIP-seq analysis.


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




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