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: [email protected] http://www.pri.wur.nl > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf > Of Michael Krogh Jensen > Sent: vrijdag 26 februari 2010 8:42 > To: [email protected] > 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 > > _______________________________________________ > 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
