User: trianglescout

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Posts by trianglescout

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Comment: C: Using edgeR or DESeq2 to analyze allele-specific expression?
... Ok, yes I see what you mean. I will start with setting the normalization factors == 1. Thanks for your input! ...
written 3.2 years ago by trianglescout40
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Answer: A: Using edgeR or DESeq2 to analyze allele-specific expression?
... For each individual, I have “total expression” (sum of M + P + counts of unknown origin)**. Originally, I planned to normalize across individuals, using this total expression (as is done in standard workflow) and then pass the correction on to the ASE counts. As an example, prior to normalization f ...
written 3.2 years ago by trianglescout40
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Comment: C: Using edgeR or DESeq2 to analyze allele-specific expression?
... Yes, the main question we are asking is: “for what genes is the paternal allele differentially expressed from the maternal allele”, and I think design <- model.matrix(~0 + individual + allele) will address this question. thanks! To complicate things further, we may also look at how ASE changes b ...
written 3.2 years ago by trianglescout40
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Using edgeR or DESeq2 to analyze allele-specific expression?
... Hi,  Does anyone have experience with standard rna-seq analysis tools (edgeR, DESeq2, etc) to detect allele-specific expression? I have a count table in which each F1 hybrid (3 biological replicates) has separate counts for the paternal and maternal allele. I am considering implementing a paired de ...
edger deseq2 ase allele written 3.2 years ago by trianglescout40

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