User: NextGenSeek

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NextGenSeek290
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6 years ago
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Posts by NextGenSeek

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Randomizing 384 Samples Among 4 96-Well Plates With Covariates
... One can think of a more balanced design. Can you please elaborate on the samples, cofactors and replicates in the study.? ...
written 6.3 years ago by NextGenSeek290
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Answer: A: Need Help For The Study Design Of A Rna-Seq Project
... Another thing to consider is, whether your fragment size is big enough. If the fragment size is smaller, paired end read may overlap significantly. In that case , smaller read length or even single end read may be worth considering. ...
written 6.5 years ago by NextGenSeek290
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Answer: A: Awards In Bioinformatics And Computational Biology
... Good idea. Here is latest paper/poster awards from RECOMB. http://recomb.org/index.php/recomb-2012-awards.html ...
written 6.6 years ago by NextGenSeek290
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Answer: A: X-Seq: Can You Provide A Listing Of The Various Applications For Sequencing Tech
... Nature BioTechnology issue had this article "The expanding scope of DNA sequencing" listing NGS applications, http://www.nature.com/nbt/journal/v30/n11/full/nbt.2421.html. (If it was behind pay wall,) we blogged this and have this list with references here http://nextgenseek.com/2012/11/did-you- ...
written 6.6 years ago by NextGenSeek290
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Answer: A: How To Compute Gene Enrichment P-Value? (Significantly More Than Expected)
... It is also worth knowing about some of the assumptions of these approaches. Here is a good paper to get started "Heading Down the Wrong Pathway: on the Influence of Correlation within Gene Sets" http://www.biomedcentral.com/1471-2164/11/574 ...
written 6.6 years ago by NextGenSeek290
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Answer: A: 10Kb Reads From Illumina Hiseq
... here is an update from Illumina at AGBT 2013. Illumina will offer it as a service by this year and as product later. http://nextgenseek.com/2013/02/illumina-to-offer-moleculo-long-read-sequencing-as-service-first-in-2013/ ...
written 6.6 years ago by NextGenSeek290
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Comment: C: Mpileup Output And Quality Scores
... Thanks for pointing to the "reference skip" definition. I still have not fully understood the "quality score" aspect of some reference skips. Here is my question. I am looking at mpileup output from RNA-Seq data from one sample. And the pileup output is something like chr1 3203517 T 30 ...
written 7.1 years ago by NextGenSeek290
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Comment: C: Mpileup Output And Quality Scores
... I am sorry about that. Can I delete this and add it as comment? ...
written 7.1 years ago by NextGenSeek290
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Mpileup Output And Quality Scores
... I am looking at mpileup output from RNA-Seq data, specifically at a location that looks like this. <<<<<<<<<<<<<<<<<<<<<<<<>>>>>><<<>><>><>>>><<<<< ...
mpileup written 7.1 years ago by NextGenSeek290
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Answer: A: Rna-Seq Review Papers
... Models for transcript quantification from RNA-Seq, Lior Pachter, preprint arXiv 2012 Computation for ChIP-seq and RNA-seq studies. Pepke, Shirley; Wold, Barbara; Mortazavi, Ali, Nature methods. 2009 6(11 Suppl):S22-32 ...
written 7.1 years ago by NextGenSeek290

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