Question: Can DEXseq be used for splicing QTL analysis?
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gravatar for rtunney2
3 months ago by
rtunney20
rtunney20 wrote:

Would it be possible (or sensible) to use DEXseq for splicing QTL analysis? If, say, instead of a factor for experimental conditions, we used 0/1/2 as a numeric vector? Would DEXseq allow you to substitute a numeric vector for the condition, and would it treat this as a numeric vector instead of a factor?

dexseq splicing sqtl qtl • 117 views
ADD COMMENTlink modified 3 months ago by Alejandro Reyes1.6k • written 3 months ago by rtunney20
Answer: Can DEXseq be used for splicing QTL analysis?
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gravatar for Alejandro Reyes
3 months ago by
Alejandro Reyes1.6k
Dana-Farber Cancer Institute, Boston, USA
Alejandro Reyes1.6k wrote:

In principle, it is possible to encode your genotypes as numeric vectors and run DEXSeq using this vector as your condition. A caveat of this approach is that you would have to run DEXSeq on every locus (or at least every time the levels of your condition change). If you have to many samples, this can become unfeasible, specially if you have many samples.

ADD COMMENTlink written 3 months ago by Alejandro Reyes1.6k
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