Moderator: andrew.j.skelton73

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Posts by andrew.j.skelton73

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Comment: C: Command not found after pip install spliceai
... I'd suggest installing via [Conda][1] [1]: https://anaconda.org/bioconda/spliceai ...
written 12 weeks ago by andrew.j.skelton736.1k
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Comment: C: Time Course RNA-Seq
... This is certainly an old post, however the approach I outlined is still valid. I'd spend some time thinking about what your experimental question is based on time. Another approach might be fit a cubic spline curve - see section 9.6.2 of the limma users guide. Mostly the *best* statistical approac ...
written 6 months ago by andrew.j.skelton736.1k
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Comment: C: Keep the paired reads whose length less than 400,000 bp
... Ah, I think you're referring to the insert size. Check out [this][1] post on filtering a bam file on insert size. Also you can use the [bbmap][2] tools to look at a histogram of your insert size for some diagnostics [1]: https://www.biostars.org/p/95822/ [2]: https://jgi.doe.gov/data-and-tools ...
written 9 months ago by andrew.j.skelton736.1k
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Answer: A: How to interpret a Stringdb interaction network of a mouse-proteomics dataset wh
... Your protein identifiers are human. Take P10809 as an example - [Uniprot Entry][1] - P10809 (CH60_HUMAN), 60 kDa heat shock protein, mitochondrial, HSPD1, Homo sapiens (Human) - [Mouse Uniprot Entry][2] - P63038 (CH60_MOUSE), 60 kDa heat shock protein, mitochondrial, Hspd1, Mus musculus (Mouse) ...
written 14 months ago by andrew.j.skelton736.1k
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Answer: A: Visualising individual humans in RNA-seq
... This is certainly a tricky problem. My favourite method for exploring what's happening with individual samples is [GSVA][1]. GSVA takes your expression matrix (genes x samples) and a set of gene sets (pathways, functions, whatever you like), and calculates a score that summarises the geneset for a g ...
written 14 months ago by andrew.j.skelton736.1k
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Comment: C: cross platform microarray normalization
... Hi, @ghataksoumyakanti - This thread is nearly 4 years old. Please open a new question with lots of detail to ensure that users can help you out! - [See here for how to ask a good question][1] [1]: https://www.biostars.org/p/75548/ ...
written 14 months ago by andrew.j.skelton736.1k
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Comment: C: Vcf produced after ApplyVSQR step
... Can you clarify if this is WES / WGS / Targeted sequencing? ...
written 17 months ago by andrew.j.skelton736.1k
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Answer: A: Vcf produced after ApplyVSQR step
... I'd check out [this post][1] which tries to explain VQSR all in one. Particularly look at the *How ApplyRecalibration works in a nutshell* section: > During the first part of the recalibration process, variants in your > callset were given a score called VQSLOD. At the same time, variants &g ...
written 18 months ago by andrew.j.skelton736.1k
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Comment: C: Vcf produced after ApplyVSQR step
... I've formatted your post so that your code blocks are more readable ...
written 18 months ago by andrew.j.skelton736.1k
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Comment: C: Investigating differentially expressed genes
... Do you have the loci of each SNP in a file? Also reference genome builds may play a role here - are they different between the RNAseq and GWAS platform? ...
written 18 months ago by andrew.j.skelton736.1k

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