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/p ackages/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 [[alternative HTML version deleted]]