Moderator: ATpoint
ATpoint ♦ 14k
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Posts by ATpoint
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... For ChIP-seq differential binding use any of the established tools such as `csaw` or `diffbind` (or others). These will require replicates. Please use **google and the search** function to look for posts and opinions on unreplicated data. This question has literally been asked dozens of times before ...
written 10 minutes ago by
ATpoint ♦ 14k
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Comment:
C: RMBlast install error
... Please use the formatting bar to highlight code and errors for better readability.
![enter image description here][1]
As for your problem, I would install with [anaconda][2].
[1]: http://oi66.tinypic.com/33kdnjt.jpg
[2]: https://anaconda.org/bioconda/rmblast ...
written 14 minutes ago by
ATpoint ♦ 14k
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... What kind of data is this? How did you produce the counts and what is the experimental setup? Are there replicates? ...
written 46 minutes ago by
ATpoint ♦ 14k
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... I would post this over at [BioC][1] to get a response from Mike Love (the DESeq2 maintainer/developer). Don't forget to post a couple of plots to show how your data are distributed and give some background information on the nature of these data, e.g. if they follow a certain distribution and how re ...
written 1 hour ago by
ATpoint ♦ 14k
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... > The distribution of my data doesn't follow a Gaussian distribution.
It probably follows the negative binomial. This is normal and expected. Check out the common differential analysis pipelines, such as DESeq2, edgeR or limma/voom. All are well-documented. ...
written 2 hours ago by
ATpoint ♦ 14k
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... Ok I see. It could be that the sharp peak is some heavily-digested non-nuclear DNA like chrM (or any other organelle DNA or parasite DNA that might be in the worm. Here is how the insert sizes look for only chrM in mouse:
![enter image description here][1]
You also see that it accumulates at short ...
written 4 hours ago by
ATpoint ♦ 14k
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... Odd plot, never seen anything like that in ATAC-seq data, and I think I've seen quiet many of them. Which dataset is that, then I quickly run it through my pipeline to see if it is indeed an odd library or a technical thing to debug. Did you filter chrM before collecting insert sizes? ...
written 5 hours ago by
ATpoint ♦ 14k
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... Did you read the [documentation][1]?
[1]: https://hicexplorer.readthedocs.io/en/latest/content/tools/hicPlotTADs.html#configuration-file-template ...
written 5 hours ago by
ATpoint ♦ 14k
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... Please use the formatting bar to highlight code and data examples for readablity.
![123][1]
[1]: http://oi66.tinypic.com/33kdnjt.jpg ...
written 5 hours ago by
ATpoint ♦ 14k
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... In mammalian genomes, DNA methylation typically occurs at CG-dinucleotides (CpG sites). If a CpG site (or any larger aggregation of CpGs like CpG islands or floats) are indeed methylated needs to be determined by experiment, e.g. via Sanger sequencing after [bisulfite][1] treatment (lowest thoroughp ...
written 7 hours ago by
ATpoint ♦ 14k
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