mouse transcriptome

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rna seq ▴ 90

@rna-seq-4145

Last seen 8.3 years ago

Hello Bioconductor, I am searching for a comprehensive list of coordinates for the mouse transcriptome. So far I have Mouse Reference Transcriptome Database http://www.genome.gov/13014330 and Tromer http://www.isrec.isb-sib.ch/tromer/. Thanks [[alternative HTML version deleted]]

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ADD COMMENT • link updated 14.5 years ago by Heidi Dvinge ★ 2.0k • written 14.5 years ago by rna seq ▴ 90

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Heidi Dvinge ★ 2.0k

@heidi-dvinge-2195

Last seen 10.3 years ago

Dear anonymous, what does this have to do with Bioconductor? Cheers \Heidi On 29 Jun 2010, at 04:11, rna seq wrote: > Hello Bioconductor, > > I am searching for a comprehensive list of coordinates for the mouse > transcriptome. So far I have Mouse Reference Transcriptome Database > http://www.genome.gov/13014330 and Tromer > http://www.isrec.isb-sib.ch/tromer/. > > Thanks > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor

ADD COMMENT • link 14.5 years ago Heidi Dvinge ★ 2.0k

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Hi Heidi, I should have been more clear. I am using RNA seq to quantify rna levels in mice. I will use the DESeq package to compare these levels but I think my experiment has identified novel transcripts. I would like to know if they are really novel, hence my question. This question should be of interest to others encountering the same problem. On Mon, Jun 28, 2010 at 11:50 PM, Heidi Dvinge <heidi@ebi.ac.uk> wrote: > Dear anonymous, > > what does this have to do with Bioconductor? > > Cheers > \Heidi > > > On 29 Jun 2010, at 04:11, rna seq wrote: > > Hello Bioconductor, >> >> I am searching for a comprehensive list of coordinates for the mouse >> transcriptome. So far I have Mouse Reference Transcriptome Database >> http://www.genome.gov/13014330 and Tromer >> http://www.isrec.isb-sib.ch/tromer/. >> >> Thanks >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]

ADD REPLY • link 14.5 years ago rna seq ▴ 90

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RNAseq-er, On Tue, Jun 29, 2010 at 8:10 AM, rna seq <rna.seeker at="" gmail.com=""> wrote: > Hi Heidi, > > I should have been more clear. I am using RNA seq to quantify rna levels in > mice. I will use the DESeq package to compare these levels but I think my > experiment has identified novel transcripts. I would like to know if they > are really novel, hence my question. This question should be of interest to > others encountering the same problem. 1. Check the AceView transcript annotations, they might be helpful: http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html 2. Check Point 3 under "While sending mail to the list" of the BioC posting guide: http://www.bioconductor.org/docs/postingGuide.html """Identify yourself. Anonymous postings are much less likely to get responses""" You might find that useful if you're looking for more help in the future. I've often been curious as to what motivates people to post anonymously on mailing lists like this one, anyway. Care to share your viewpoints? Cheers, -steve -- 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

ADD REPLY • link 14.5 years ago Steve Lianoglou ★ 13k

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