dear all: it seems writeFasta can not allow RNA sequences. writeFasta(RNAStringSet(x, use.names=TRUE),"miRNA") Error in function (classes, fdef, mtable) : unable to find an inherited method for function "writeFasta", for signature "RNAStringSet" -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253

Hi, On Sun, Mar 18, 2012 at 3:49 PM, wang peter <wng.peter at="" gmail.com=""> wrote: > dear all: > ? ? ? ? it seems writeFasta can not allow RNA sequences. > > > writeFasta(RNAStringSet(x, use.names=TRUE),"miRNA") > Error in function (classes, fdef, mtable) ?: > ?unable to find an inherited method for function "writeFasta", for > signature "RNAStringSet" Interesting. For now, Biostrings::write.XStringSet (which writeFasta calls internally) handles it. Not sure if it's intentional to not support RNA* in the ShortRead functions[*] but you can at least use Biostrings::write.XStringSet to do what you need for now. -steve [*] maybe it is intentional since no sequencers I know of will read a "U" as most (all) incorporate dNTPs (not rNTPs) while reading ... just stabbing at the dark on this one, though. -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact