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Comment: Pseudogene - scarce info
by
ATpoint
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This reminds me strongly on my "masters" courses (doesn't deserve that name tbf). "Here is some poorly-described project with little to no …
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There is no "better" is my experience. It always depends on the dataset. Try both and integrate your biological knowledge to decide which m…
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Aleksandra
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I just wrote that I misunderstood your initial question.
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If I understand correctly, you see increased signal at TSS sites compared to control (taller peaks in browser). However, 92% of the 450 siS…
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this question is a little similar to your previous question (https://www.biostars.org/p/9614638/). just as added info, here is a tool calle…
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As mentioned above, I just got the raw fastq files from the ftp site listed.
Comment: DESeq2 on metagenome KO counts
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This statement makes zero sense in response to what I wrote.
Comment: DESeq2 on metagenome KO counts
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Aleksandra
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I focused on the fact that DESeq2 models overdispersion, but overlooked its implicit assumption: normalisation works when the main source o…
Comment: DESeq2 on metagenome KO counts
by
Aleksandra
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180
Thank you very much. I mistakenly drew a superficial analogy. I equated KO counters with gene counters.
Comment: DESeq2 on metagenome KO counts
by
ATpoint
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Both vst or logcpm will favor expression level (magnitude of counts) rather than differences in a hclust/heatmap. For differences you need …
Comment: DESeq2 on metagenome KO counts
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ATpoint
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The DESeq2 developer has advised many times against DESeq2 for metagenomics. Please search for related posts over at support.bioconductor.o…
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I wouldn’t use DESeq2 on aggregated raw counts per KO, because doing so means accepting two pretty big assumptions:
1. All genes with t…
Comment: DESeq2 on metagenome KO counts
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Aleksandra
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(I apologise for my previous reply; I wanted to be as detailed as possible)
DESeq2 handles KO counts perfectly well. For a time-series des…
Comment: DESeq2 on metagenome KO counts
by
Aleksandra
▴
180
I apologise for how that sounded; I wanted to be as detailed as possible.
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