Hello Vanessa, On 02/24/2012 10:45 AM, Corby, Vanessa wrote: > Hello Herve and Matt, > > After looking through the Bioconductor documentation for the BeeBase > assembly 4 package Herv? posted (information on the Apis 4 annotation > stored in Biostrings objects), the documentation for the org.Hs.eg.db > Annotation database documentation, the bioconductor mailing list, the > BSgenome documentation, and the goseq documentation, I am still very > confused about whether I can use the assembly 4 package that Herv? > posted in goseq. Just to clarify, goseq is not my package so I can't "post" anything in it, whatever that means. I assume you are talking about the BSgenome.Amellifera.BeeBase.assembly4 package that I made and that is part of Bioconductor. > The reason that I want to use the assembly 4 data is > that I would presume that it will have more current information than the > natively supported (by goseq) Apis release 2. It's a more recent assembly so I would expect it to be more accurate (i.e. closer to reality). > > So, here are my questions: > > 1.Will release 4 offer much improvement over release 2? If this is not > the case, then the next two questions are moot. It's just a more recent assembly, with all what that implies. > > 2.Do I need to get information on the transcript lengths and the > associations between the geneids and GO terms for the Apis 4 release and > build 2 new files of this information for goseq to use? I'm not familiar with the goseq package so I'll let Matt answer this. > Is that > information available (perhaps through UCSC or Baylor?s site for the > honeybee projects)? Can I use Bioconductor for this if I have the > annotation database file Herv? posted? The BSgenome.Amellifera.BeeBase.assembly4 package only contains the DNA sequences of Apis 4 release. It does *not* contain annotations for this assembly. One advantage of using the BSgenome.Amellifera.UCSC.apiMel2 package instead is that you have an easy access to a world of annotations for this genome thru the UCSC genome browser. Too bad that the UCSC folks have not plans to support apiMel4: https://lists.soe.ucsc.edu/pipermail/genome/2007-October/014763.html apiMel2 is 7 year old now! Note that the GenomicFeatures and rtracklayer packages make it really simple to import and work with those annotations in R/Bioconductor. > > 3.Do I just have to rename the Apis 4 genome package that Herv? posted > in order to use it in goseq (I see that there are several naming > conventions on the Annotation Data packages)? I'll let Matt answer this. > > You can see that some of these questions are more appropriate for Herv? > and some for Matt, so I decided to email both of you. Some of these > issues arise simply because I?ve only been successful with the example > in the goseq documentation (using the org.Hs.eg.db Annotation database). > Others arise because I am just very new to R and the Bioconductor packages. For what is worth, I don't think there is any org.* package for Bee (would probably be named something like org.Am.eg.db if there was one). And if there was one, you would need to double-check that the annotations in it are actually compatible with whatever genome assembly you finally decided to use. > > Thanks for any help you can offer. And apologies if this is the 100^th > time you?ve received an email about this from newbies such as myself. No problem. Wish I could help more. I'm cc'ing the Bioconductor mailing list (hope you don't mind). It's a better place to ask questions like this as other people might be able to help and also the whole discussion will be archived and searchable for further reference. Cheers, H. > > Vanessa Corby-Harris > > Research Molecular Biologist > > USDA-ARS > > Carl Hayden Bee Research Center > > 2000 E. Allen Rd., Tucson, AZ 85719 > > (520) 647-9269 > > This electronic message contains information generated by the USDA > solely for the intended recipients. Any unauthorized interception of > this message or the use or disclosure of the information it contains may > violate the law and subject the violator to civil or criminal penalties. > If you believe you have received this message in error, please notify > the sender and delete the email immediately. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319