Moderator: andrew.j.skelton73

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Posts by andrew.j.skelton73

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Comment: C: retrieve normalised count data from DESeq2
... Check the rownames on your input matrix. If they're not set, then they'll default from `1:n` ...
written 28 days ago by andrew.j.skelton735.5k
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Answer: A: Extracting this data frame from a .vcf file
... GATK has a tool for that, see [VariantsToTable][1] [1]: https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantutils_VariantsToTable.php ...
written 5 weeks ago by andrew.j.skelton735.5k
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Answer: A: GATK ASEReadCounter: Downstream analysis for identifying allele specific express
... Late to the party on this post, but as @prasundutta87 alludes to, ASEReadCounter is doing exactly what it was intended to do. The best guide I've seen to performing the statistics around ASE, is from Mike Love's [specific guide][1], and it's worth looking at [this thread][2] for Aaron Lun's answer t ...
written 9 weeks ago by andrew.j.skelton735.5k
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Comment: C: batch effect in RNAseq analysis using tophat cufflinks pipeline
... That's fair, Cufflinks (Faux Tiling) and StringTie (Network Flow) use different methodologies, so you're right that TopHat can be substituted with HISAT2 or STAR. Bit of an oversight on my part. ...
written 10 weeks ago by andrew.j.skelton735.5k
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Answer: A: MSTRGs are plaguing my RNA-Seq analysis
... This has always been an issue as far as novel transcript discovery goes, you can see a lot of hits. Keep in mind that the vast majority of these are very slight changes to known transcripts and splice events, which are generally meaningless. When performing this kind of analysis I generally get rid ...
written 10 weeks ago by andrew.j.skelton735.5k
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Comment: C: batch effect in RNAseq analysis using topcoat cufflinks pipeline
... [See comment from the Tophat author][1] ![enter image description here][2] [1]: https://twitter.com/lpachter/status/937055346987712512 [2]: https://i.ibb.co/ydfBD23/Screenshot-2019-01-08-at-08-26-38.png ...
written 10 weeks ago by andrew.j.skelton735.5k
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Answer: A: batch effect in RNAseq analysis using topcoat cufflinks pipeline
... Tophat is deprecated, avoid if possible. ------------------------------------------------------------------------ Firstly, visualise your problem with a PCA - this will give you clues as to where your primary variation is coming from, and if a batch effect is clearly present. Try one of the followi ...
written 10 weeks ago by andrew.j.skelton735.5k
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Comment: C: get calls in R
... Hi @HG, The community is not here to provide tailored programming solutions/ tutorials. Please amend your post to show some reproducible data to your question, along with code showing what you've tried. ...
written 12 weeks ago by andrew.j.skelton735.5k
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Comment: C: ATYPICAL VOLCANO PLOT RNA SEQ
... It would be helpful if you included code for your analysis, did you use `lfcShrink`? Are your samples all from the same experiment? What did you PCA show? ...
written 4 months ago by andrew.j.skelton735.5k
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Answer: A: eQTL analysis considering P-values
... For generic QTL analyses, I'd recommend the MatrixEQTL package and associated methodology. It's blazing fast providing you have the right LINPACK libraries. [Website][1] / [Paper][2] / [Package (CRAN)][3] Check out the website for some useful examples and configurations [1]: http://www.bios. ...
written 4 months ago by andrew.j.skelton735.5k

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