Quick illumina question
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Lynn Amon ▴ 110
@lynn-amon-1601
Last seen 8.1 years ago
I have made annotation packages for the Illumina Refseq beadchips for human and mouse. I submitted these to Bioconductor but I guess they didn't make the cut. The compressed files are 10 MB. If you are interested, I could try emailing them to you. Lynn Amon Research Scientist Department of Pathology University of Washington > Message: 16 > Date: Fri, 21 Jul 2006 21:53:41 -0400 > From: Sean Davis <sdavis2 at="" mail.nih.gov=""> > Subject: [BioC] Quick illumina question > To: Bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <c0e6fd65.162f%sdavis2 at="" mail.nih.gov=""> > Content-Type: text/plain; charset="US-ASCII" > > I have been looking at some raw illumina data. The results are reported > with the illumicode id. I can't seem to find where I can convert the > illumicode to the actual associated sequence. Can someone who is using > illumina arrays point me in the right direction? > > Thanks, > Sean
Annotation Annotation • 655 views
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@sean-davis-490
Last seen 6 weeks ago
United States
Thanks, Lynn, for the offer. Just to clarify what we do, we actually reannotate the probes (via blast against refseq, ensembl, dbEST, unigene_unique, various genome builds, etc.) for all the arrays that we use and then use a relational database for storing and querying probe information and annotation. This gives us mapping information down to the base pair and the ability to link in any annotation we like, which is often useful, particularly for sticky issues like probe performance (or lack thereof) and cross-platform comparisons. In this particular case, it turns out that the "bead manifest" is the file that I needed, which Illumina was able to provide via their technical support after a few directed questions. Sean On 7/24/06 12:46 PM, "Lynn Amon" <lynnamon at="" u.washington.edu=""> wrote: > I have made annotation packages for the Illumina Refseq beadchips for > human and mouse. I submitted these to Bioconductor but I guess they > didn't make the cut. The compressed files are 10 MB. If you are > interested, I could try emailing them to you. > Lynn Amon > Research Scientist > Department of Pathology > University of Washington > > >> Message: 16 >> Date: Fri, 21 Jul 2006 21:53:41 -0400 >> From: Sean Davis <sdavis2 at="" mail.nih.gov=""> >> Subject: [BioC] Quick illumina question >> To: Bioconductor <bioconductor at="" stat.math.ethz.ch=""> >> Message-ID: <c0e6fd65.162f%sdavis2 at="" mail.nih.gov=""> >> Content-Type: text/plain; charset="US-ASCII" >> >> I have been looking at some raw illumina data. The results are reported >> with the illumicode id. I can't seem to find where I can convert the >> illumicode to the actual associated sequence. Can someone who is using >> illumina arrays point me in the right direction? >> >> Thanks, >> Sean
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