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Forum: General 07-13-2011, 11:50 AM
Replies: 2
Views: 3,538
Posted By EMeyer
DESeq: GLMs for RNA-Seq with interaction terms

I have a reasonably large RNA-Seq dataset for a non-model plant, and want to fit a GLM with interaction terms:
expression ~ treatment + time + treatment:time

In theory, I should be able to test...
Forum: Bioinformatics 07-18-2008, 01:04 PM
Replies: 4
Views: 7,291
Posted By EMeyer
Thanks again. Its performing well on my dataset,...

Thanks again. Its performing well on my dataset, giving a slightly larger average contig size than Newbler and a distribution of contigs that is both narrower and more normal. The big drawback I...
Forum: Bioinformatics 07-17-2008, 12:57 PM
Replies: 4
Views: 7,291
Posted By EMeyer
Thank you, I am impressed with the level of...

Thank you, I am impressed with the level of documentation for that package! I will give it a shot.

I didnt see a publication of the method itself. Do you know if there is one in preparation / in...
Forum: Bioinformatics 07-17-2008, 11:52 AM
Replies: 7
Views: 7,417
Posted By EMeyer
Mark, I know its not what you were asking...

Mark,

I know its not what you were asking for in this post, but if a set of 454 reads (~600k raw reads) would be useful for testing Euler-SR, I'd be happy to share those with you in exchange for a...
Forum: Bioinformatics 07-17-2008, 11:34 AM
Replies: 12
Views: 5,321
Posted By EMeyer
de novo assembly of transcriptomes

Hi All,

It strikes me that most discussions about assembly -- and perhaps even most assembly software -- are centered around assembly of genomes. So I wonder about what special challenges might...
Forum: Introductions 07-16-2008, 04:49 PM
Replies: 0
Views: 1,718
Posted By EMeyer
Hello from Austin TX

Hi All,

Im a postdoc working at University of Texas in Austin. We're pyrosequencing the transcriptome of a reef building coral, and using SOLiD for gene expression analysis. So this looks great...
Forum: Bioinformatics 07-16-2008, 03:11 PM
Replies: 4
Views: 7,291
Posted By EMeyer
Interpretation of Euler-SR assembly (454 transcriptome)

Hi all,

We've recently completed a run of 454 sequences from the transcriptome of a reef-building coral, and I am in the process of attempting de novo assembly. Since it seems Euler-SR does...
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