Moderator: andrew.j.skelton73
andrew.j.skelton73 ♦ 6.1k
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Posts by andrew.j.skelton73
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... I'd suggest installing via [Conda][1]
[1]: https://anaconda.org/bioconda/spliceai ...
written 12 weeks ago by
andrew.j.skelton73 ♦ 6.1k
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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.skelton73 ♦ 6.1k
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... 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.skelton73 ♦ 6.1k
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... 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.skelton73 ♦ 6.1k
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... 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.skelton73 ♦ 6.1k
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... 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.skelton73 ♦ 6.1k
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750
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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.skelton73 ♦ 6.1k
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... 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.skelton73 ♦ 6.1k
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750
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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.skelton73 ♦ 6.1k
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... 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.skelton73 ♦ 6.1k
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