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: [email protected] [mailto:[email protected]] On Behalf Of [email protected] Sent: Thursday, March 19, 2009 3:24 PM To: [email protected] 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
