User: scottdaniel25

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Tucson, AZ
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3 months ago
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Molecular and Cellular Biology Ph.D. Graduate Student at the University of Arizona.

Posts by scottdaniel25

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Cuffquant / Cuffnorm - Why are some feature counts exactly the same?
... Hi, I'm getting some weird counts after aligning RNA-seq to some bacterial genomes with bowtie2 and then counting / normalizing with cuffquant / cuffnorm respectively. I'm getting something like this with some of my output: Feature A - Species 1 4440.79 Feature B - Species 2 4440.79 Fe ...
htseq-count cuffnorm rna-seq cuffquant written 4 months ago by scottdaniel2530
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Answer: A: How Do I Estimate The Number Of Rna-Seq Reads Needed To Detect Differential Expr
... So I think I sort of answered it... from a very rough perspective. What I did was use R to simulate Fisher.test's for differential expression based on number of reads. I figured it would give a good approximation of changing the range of reads (i.e. from 1 to 45 vs 1 to 75 as stated in the problem) ...
written 3.3 years ago by scottdaniel2530
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How Do I Estimate The Number Of Rna-Seq Reads Needed To Detect Differential Expression?
... x-posted at stack exchange's 'cross calidated' here. Currently, our samples are going to get at least 30 million reads each. Given that we have 3 biological replicates per condition, that gives us 90 million reads. Let's say we only get 50% of those aligned and only count 100bp segments (even thoug ...
reads differential-expression rna-seq written 3.3 years ago by scottdaniel2530 • updated 6 months ago by Biostar ♦♦ 10
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Comment: C: Normalizing Pertinent Groups
... Thanks for the great answer. I edited the post to include platform information. I have done the in silico comparison and the only thing that splitting them up into groups is improve the p-values slightly, it doesn't change the order or significance of the mis-regulated genes. ...
written 4.9 years ago by scottdaniel2530
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Normalizing Pertinent Groups
... In an experiment on fruit flies, I have a set of expression data of four groups of larvae: 1. 0 day old mutants 2. 3 day old mutants 3. 5 day old mutants 4. 0 day old wild-type (The wild-type does not have 3 or 5 day olds because by that time wild-type larvae have pupated) I have a quandary with no ...
limma microarray written 4.9 years ago by scottdaniel2530 • updated 4.9 years ago by seidel6.0k

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