Hi Martin, I am also working in ChIP-seq analysis. We have recently released our R Package CSAR.
CSAR normalizes the sample and control data to have the same coverage. So, to have an estimation of the coverage is important. However, the coverage that you will estimate from the aligned read file may be different to the coverage of your data after filtering/processing. We usually also use the coverage for each chromosome to detect any bias in the sequencing /analysis process. If the coverage of each chr is not similar probably there was some problem with the sequencing (or the quality of the genomic sequence of a particular chr). If the coverage is the same, but the number of detected "peaks" is extremely different between chrs, we may think that the analysis process could introduce some bias. Greetings, Jose Dr. Jose M Muino Plant Research International B.V. P.O. Box 619, 6700 AP Wageningen, The Netherlands Phone: +0317-481122. E-mail: [email protected] http://www.pri.wur.nl > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf > Of Martin Morgan > Sent: donderdag 11 februari 2010 20:23 > To: Droit Arnaud > Cc: [email protected] > Subject: Re: [Bioc-sig-seq] ShortRead sequences > Are you anticipating calling something like 'coverage' as an > immediate first step? We have been thinking about > implementing high-level command like coverage("file.bam", > param=param), and it would be good to know what the the use cases are. > > Martin > > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
