[BioC] How to use cutome reference genome?

Yan He [guest] guest at bioconductor.org
Fri Aug 31 11:31:16 CEST 2012

I am trying to use the MEDIPS package in Bioconductor. The tutorial says that one of the supplied reference genomes must be used. Does anyone know how to produce a custom reference genome in case one's genome of interest is not one that list? I am directed to BSgenome by the same question posted by Kelly V.. However, the BSgenome is based on the Biostrings-based genome data package. What should I do if I have my own sequenced genome sequence and not published yet?

Thanks very much for your help!


 -- output of sessionInfo(): 

R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

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