Hi Hiram, Yes. I thought that 'masked' option would invoke 'repeat masking' on the sequence (extracted using nibFrag) and looks like that is not the case. Am I right?
Thanks Jyoti -----Original Message----- From: Hiram Clawson [mailto:[email protected]] Sent: Monday, January 12, 2009 11:21 PM To: Shah, Jyoti K. Cc: [email protected] Subject: Re: [Genome] nibFrag Good Evenin Jyoti: I guess it depends upon where you obtained the nib files from ? What nib files are you using and how do you operate the command ? The option -masked does the following: -masked - use lower case characters for bases meant to be masked out which means it prints lower case characters in masked regions. What do you mean "not able to repeat mask sequence" ? Are you trying to run RepeatMasker ? --Hiram Shah, Jyoti K. wrote: > Hi UCSC team, > > I am using your nibFrag tool to extract parts of a sequence. I am not > able to repeat mask sequences using you 'masked' or 'hardMasked' > options. Do they really mask the sequence or they just ignore the parts > of sequence that have been pre-masked? > > Thanks > Jyoti Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
