[Bioc-sig-seq] Arabidopsis reference genome

[Muino, Jose]

Hi,

TAIR9 is the best option, it is the standard in the field. But to map
the reads I will use or BWA, Bowtie or SOAP (v1, v2)

Dr. Jose M Muino
Plant Research International B.V.
Droevendaalsesteeg 1
P.O. Box 16, 6700 AA 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 Michael Krogh Jensen
> Sent: vrijdag 26 februari 2010 8:42
> To: bioc-sig-sequencing at r-project.org
> Subject: [Bioc-sig-seq] Arabidopsis reference genome
> 
> 
> Hi,
> 
> New in next-gen sequencing data analysis I would like to know 
> if any of you have experience with the Arabidopsis TAIR9 
> annotation for reference mapping of Arabidopsis single-end 
> reads using - for instance - ELAND? If not using the TAIR9 
> annotation I would like to know what other Arabidopsis 
> reference genome to be used.
> 
> Thanks in advance.
> 
> Best, 
> 
> Michael
> 
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