User: Vincent Laufer
Vincent Laufer • 1.0k
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Posts by Vincent Laufer
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... this is interesting - of course the bulk of the literature of which I am aware derives an understanding of these levels from the number of effectively independent markers.
so would be odd to use a pig based threshold unless they have similar levels of LD and numbers of haploblocks ...
written 15 days ago by
Vincent Laufer • 1.0k
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Comment:
C: GWAS, quantitative traits
... perhaps my answer to this post can help you
https://www.biostars.org/p/176238 ...
written 9 weeks ago by
Vincent Laufer • 1.0k
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... Do you have the pathways annotated?
In what ways do you want to compare them? ...
written 10 weeks ago by
Vincent Laufer • 1.0k
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... @k.woolf -
*Because your goals still rely on quantitative comparisons,* I would recommend you use either unique reads only, or that you use a published method of partial transcript estimation. To explore this, let's think about two simple approaches, and try to identify problems.
Consider a singl ...
written 10 months ago by
Vincent Laufer • 1.0k
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... Hey,
I think I understand, but could you elaborate on the format of the referenced genome file? ...
written 10 months ago by
Vincent Laufer • 1.0k
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... not at all. i will remember this for the future. thanks. ...
written 10 months ago by
Vincent Laufer • 1.0k
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... Hi all,
I was hoping to crowdsource ideas to help get a high school student started thinking about biology and informatics.
The student I have in mind is a gifted computer programmer, my understanding is he can already work on games requiring 3D modeling, etc. His knowledge of math and biology do ...
written 10 months ago by
Vincent Laufer • 1.0k
• updated
10 months ago by
h.mon ♦ 25k
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... Although this does not address your initial question, I wanted to propose a downstream QC step that can help you decide if the approach you do use was successful or not.
After finding a mapping that is acceptable (for example the 2-step assembly per ecotype approach recommended by @genomemax in his ...
written 10 months ago by
Vincent Laufer • 1.0k
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... I agree with the comment above; i.e. we need to know what exactly you mean. Is what you want to say "how can I map the location of each CNV to one or more genes, provided they overlap?"
Second, I would like to ask *what kind of data you have* (e.g. whole genome sequencing / microarray / multiple / ...
written 10 months ago by
Vincent Laufer • 1.0k
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... Hello all,
Is there a function written in R or another language of the form:
Variance_Explained <- get_var_exp(effect_size, minor_allele_frequency, [other args])
Specifically, on page 25 of the supplemental methods of Stahl et al. 2012 (see https://www.nature.com/articles/ng.2232 ), an eq ...
written 11 months ago by
Vincent Laufer • 1.0k
• updated
10 months ago by
zx8754 ♦ 7.5k
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For Varying Sample Size vs Read Depth, Read Length, and Single vs Paired end to optimize DE analysis of RNA-Seq
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