[Bioc-sig-seq] ShortRead sequences

[Muino, Jose]

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: jose.muino at wur.nl
http://www.pri.wur.nl 
 

> -----Original Message-----
> From: bioc-sig-sequencing-bounces at r-project.org 
> [mailto:bioc-sig-sequencing-bounces at r-project.org] On Behalf 
> Of Martin Morgan
> Sent: donderdag 11 februari 2010 20:23
> To: Droit Arnaud
> Cc: bioc-sig-sequencing at r-project.org
> 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
> 
>