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Detecting highly variable genes within replicates
Detecting highly variable genes within replicates
A: Detecting highly variable genes within replicates
How to set a threshold for coefficient of variation in RNA-seq?
What is Deepvariant default filtering values ?
Answer: EdgeR - relationship between logFC and coefficients
Answer: EdgeR - relationship between logFC and coefficients
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Answer: DESeq2 error
by
ATpoint
82k
At least one group needs replication. That is the short answer. For a longer answer add details on experimental design.
Comment: When should I use R-MarkDown over R-Script ?
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ATpoint
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What is your motivation to ask? Add some context. Beyond that, always use Rmd unless you write package code.
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ATpoint
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RNA-seq is typically analyzed on gene rather than transcript level. Are your counts gene or transcript?
Comment: EdgeR - relationship between logFC and coefficients
by
gBioStar5
• 0
Thanks a lot, this was very helpful. I'll keep that in mind.
Answer: EdgeR - relationship between logFC and coefficients
by
Gordon Smyth
★ 7.1k
Results presented by topTags() are on the log2 scale. Coefficients stored internally in the DGELRT object are on the loge scale. If you con…
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size_t
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run command `explorer.exe .` in wsl terminal, and then drag file to folder
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Hi Ricardo! CAP3 is an 'older' overlap assembler from 1999 which is perfectly suited for these kinds of 'small' tasks. I used it last in my…
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Jesse
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That's really handy, and much more of a general solution than stripping off the directory names! So yifangt86, if you're on Linux you can …
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Are you missing a `"` at the end of the URL. Doing wget -O test.out "https://www.ebi.ac.uk/ena/portal/api/filereport?accession=PRJNA43…
Comment: Different output for read length
by
marco.barr
▴ 100
very strange, I double checked the BAM file and it is the same one I used for your request. Are the commands I wrote above correct? How is …
Comment: Different output for read length
by
Pierre Lindenbaum
161k
the first read as a length of 1747, i wonder how you can just find '50' $ wget -qO - "https://gist.githubusercontent.com/Macdot3/4650…
Comment: Problem with Seurat package in PercentageFeatureSet function
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bk11
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Yes, `CreateAssayObject` function is used for only expression matrix.
Comment: Different output for read length
by
marco.barr
▴ 100
Here is my result, I hope you can see it. [https://gist.github.com/Macdot3/4650243a10540d8c06f728ffc16a136c][1] [1]: https://gist.gith…
Comment: Different output for read length
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marco.barr
▴ 100
I just published my link on paste, why can't I see my public paste on the site?
Comment: cellranger error message
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Max
• 0
I'm having a similar issue. The sample_id matches the filename prefix before _S1_L001, but I get the error: Log message: Requested sample(s…
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