Dear Carlos,

Yes, you will need to forge BSgenome for lettuce.  Here is the documentation on how to forge a BSgenome http://www.bioconductor.org/packages/release/bioc/vignettes/BSgenome/inst/doc/BSgenomeForge.pdf.

I cced Herve Pages and the bioconductor list for input on forging a BSgenome using scaffolds.

Best regards,

Julie

On 4/11/13 1:34 AM, "Carlos Galeano" <galeano@ucdavis.edu> wrote:

Dear Lihua,

I am working in lettuce genetics. At moment I am developing a double digestion genotyping by sequencing (GBS) methodology. I would like to compare my result with the in-silico restriction analysis.  Therefore, I have found your package REDseq very usefull. Based on the user guide, I have to input my genome in GSgenome format, isn’t it? However, we have a preliminary assembly (scaffolds) of lettuce, and I guess that to forge a BSgenome I need pseudochromosomes, isn’t it?
So, the question is how can I use REDseq with my scaffods?

Many thanks,

Carlos



Carlos H. Galeano M.
Postdoctoral researcher
Genome Center, University of California, Davis
451 East Health Science Drive
Davis, CA 95616-8816
Phone (530) 752-8889
Fax (530) 754-9658



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