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Answer: Differential Expression Analysis using DESeq2 in R
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![Here is the code I am using for the analysis][1]
[1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
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According to the link:
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Okay, that shows us the problem, but not what we need to solve it.
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In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1].
[1]: https://groups.goo…
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Yes, but I think the problem is what to do when MAF = 0.5
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In Plink, A1 is usually a minor allele and A2 a major allele.
.frq (basic allele frequency report)
Produced by --freq.
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I briefly looked at those genes on a genome browser -- there are a lot of repeat elements in those genes, meaning a lot of counts assigned …
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