Moderator: andrew.j.skelton73

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Posts by andrew.j.skelton73

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Answer: A: Question regarding Bioinformatics with R and large comparisons
... Chances are, there's already a tool that will do / partly do what you want. I'd suggest looking at [Omicstools][1] for a specific look at what's around, and how they could fit to your problem. It sounds like your problem is sequence classification? - It might be worth looking in the BLAST direction, ...
written 23 hours ago by andrew.j.skelton734.8k
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Comment: C: stringTie Warning message
... Have you looked at your reference GFF file in IGV at the coordinates listed? ...
written 3 days ago by andrew.j.skelton734.8k
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Answer: A: CNV calling using ExomeDepth
... ExomeDepth works on coverage, and there's functionality within ExomeDepth to determine an optimal reference / set of references to use. See section 5 [here in the vignette][1]. ExomeDepth typically goes with highly correlated samples, hence it's essential that your samples are from the same batch of ...
written 5 days ago by andrew.j.skelton734.8k
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Comment: C: Linkage analysis with whole -exome sequencing data
... Another one I came across recently is [SEQLinkage][1] [1]: http://www.bioinformatics.org/seqlink/ ...
written 5 days ago by andrew.j.skelton734.8k
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Answer: A: Some explanation about what a paired-end sequencing really means
... Always easier to illustrate with an image, from [here][1]. The grey represents the fragment, and each end of the fragment is sequenced. This allows more accurate mapping, particularly of repetitive regions. There's also a great animation [here][2] that illustrates the concept of Illumina paired end ...
written 11 days ago by andrew.j.skelton734.8k
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Comment: C: retrospective trio analysis from WGS SNPs
... From the [paper][1]: > The framework underlying the KING approach to relationship inference > centres on modelling genetic distance between a pair of individuals as > a function of their allele frequencies and kinship coefficient I don't believe that a panel is used, rather a random sele ...
written 13 days ago by andrew.j.skelton734.8k
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Answer: A: Removing batch effects between Affymetrix and Agilent platforms using ComBat
... I suggest you have a look at my answer [here][1], which may clarify some batch correction limitations. [1]: https://www.biostars.org/p/311168/#311200 ...
written 25 days ago by andrew.j.skelton734.8k
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Comment: C: Surrogate variable analysis: ask for a practical example
... While not applicable to SVA specifically, additive models for correction of nuisance variables was something that peaked my interest a while ago. I got a fantastic example from Aaron Lunn on Bioconductor support that might help you understand [here][1] [1]: https://support.bioconductor.org/p/69 ...
written 25 days ago by andrew.j.skelton734.8k
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Answer: A: Surrogate variable analysis: ask for a practical example
... Surrogate variables, batch effects, technical effects in general are better seen as an experiment wide visualisation, such as with a PCA - One gene is not indicative of unexpected variation. The example you outline could be anything, `sample 3` may be an outlier, or it could be completely expected i ...
written 25 days ago by andrew.j.skelton734.8k
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Comment: C: Deseq2 batch effect design issue
... As @JJ has already told you, this design cannot be made balanced. I'd suggest analysing the experiments separately, and if you really feel they're comparable, try a non-parametric approach such as [RankProd][1] for looking at the differences in respective fold changes. [1]: https://www.biocondu ...
written 26 days ago by andrew.j.skelton734.8k

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Teacher 21 days ago, created an answer with at least 3 up-votes. For A: Why is the gene name repeated many times in my file?
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Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Why is the gene name repeated many times in my file?
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Appreciated 6 months ago, created a post with more than 5 votes. For A: Find SNPs in the exome from WGS data
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