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Recent Replies
Comment: combine VCF from diploid reference/haplotypes for the same sample
by
cmdcolin
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4.3k
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…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space?
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aj123
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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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ATpoint
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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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180
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
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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
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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
89k
The DESeq2 developer has advised many times against DESeq2 for metagenomics. Please search for related posts over at support.bioconductor.o…
Answer: DESeq2 on metagenome KO counts
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andres.firrincieli
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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
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Aleksandra
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I apologise for how that sounded; I wanted to be as detailed as possible.
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A comment on: "*Wonky analysis is possible even with open-source R libraries.*"
True - and arguably, the risk of a wonky analysis is actua…
Comment: GUI commercial software for 10x single cell gene expression analysis
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`Trailmaker` likely only supports Parse's evercode data. <br>
`BioTuring` does not appear to have published pricing. <br>
`Rosalind` appear…
Answer: GUI commercial software for 10x single cell gene expression analysis
by
firestar
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Found a few more when I asked around. I have no idea how good or bad these are. If anyone has used these or knows more about these, feel fr…
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> I performed a standard proteomics screening workflow
What database did you use to search against? Perhaps you are using an old (not so c…
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No, it's unrelated. Doublets in 10x happen if two cells get enclosed into the same GEM droplet. This has nothing to do with how flow cytome…
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