Moderator: dariober
dariober ♦ 10k
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Posts by dariober
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... Thanks for sharing! Partly as a shameless plug... I wrote [ASCIIGenome](https://asciigenome.readthedocs.io/en/latest/description.html) because it covers a need that none of the others satisfies: It runs on the terminal without graphical interface. Since I work almost exclusively on remote servers, a ...
written 6 days ago by
dariober ♦ 10k
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... Two years later... +1! I spent the last 2 hours trying to figure out why my dumb average of phred scores didn't match NanoPlot's (+1 also to that) until I dug into its code and eventually found this thread. ...
written 13 days ago by
dariober ♦ 10k
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... I haven't tried it by I think you should use the `filename` parameter:
vcf_reader = vcf.Reader(filename='input.vcf.gz') ...
written 6 weeks ago by
dariober ♦ 10k
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... > There is no climate crisis
Are you saying that the climate is not changing or that the change is not a big deal? Either way, this is a difficult position to hold as there is tons of scientific research supporting the case of the climate crisis. ...
written 7 weeks ago by
dariober ♦ 10k
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... You are right, well spotted - I corrected my answer ...
written 10 weeks ago by
dariober ♦ 10k
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... Granted that mine is a guess since I haven't read the paper...
> the authors have somehow integrated RPKM along with the edgeR package
Mmm... no, I don't think so... They used edgeR for detecting differentially expressed genes and they considered as biologically relevant genes with FDR < 0.0 ...
written 10 weeks ago by
dariober ♦ 10k
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Comment:
C: Job management programs
... Hi Devon, would you mind expanding on that? I mean, I know you can install slurm on a single node, but is it something reasonably doable by someone without admin rights and without investing a fair bit of effort maintaining slurm over time? ...
written 10 weeks ago by
dariober ♦ 10k
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Answer:
A: Job management programs
... Depending on how much effort you want to invest, you could run your program(s) via [snakemake](https://snakemake.readthedocs.io/en/stable/) and let snakemake handle parallelism and job dependencies. There will be a learning curve but in my opionion is totally worth it.
Alternatively, with `xargs` ( ...
written 10 weeks ago by
dariober ♦ 10k
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... Hi- For a discussion about adapter trimming you may find this thread useful https://www.biostars.org/p/212136/
> there doesn't seem to be such a clear consensus on a good minimum read length except to say that overly short reads can cause spurious alignment
Spurious alignments should have zero ...
written 3 months ago by
dariober ♦ 10k
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... The [facets](https://github.com/mskcc/facets) package detects copy number variants and gives you the purity and ploidy estimates.
If interested, I also wrote a wrapper to run the analysis as a single line command, see [cnv_facets](https://github.com/dariober/cnv_facets). ...
written 5 months ago by
dariober ♦ 10k
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