Moderator: ATpoint

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ATpoint14k
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Posts by ATpoint

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Comment: C: what is the best way to calculate significant differences in tss profiles?
... 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 ATpoint14k
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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 ATpoint14k
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Comment: C: what is the best way to calculate significan differences in tss profiles?
... 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 ATpoint14k
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Comment: C: Is right normalize metabolomics "counts" by Variance Stabilized Transformation u
... 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 ATpoint14k
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Comment: C: statistical analyses for tanscriptomes
... > 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 ATpoint14k
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Comment: C: Insert size of -20bp with ATAC-seq?
... 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 ATpoint14k
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Comment: C: Insert size of -20bp with ATAC-seq?
... 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 ATpoint14k
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Comment: C: hicexplorer hicPlotTADs configuration file
... 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 ATpoint14k
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Comment: C: Understanding 9th field of Bam file - insert size?
... 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 ATpoint14k
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Answer: A: how to visualize DNA methylation regions in a given genome sequence??
... 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 ATpoint14k

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