User: al-ash
al-ash • 0
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Posts by al-ash
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... I might not understand the command `AlignmentToFilter[, -seq(1, ncol(AlignmentToFilter), by=3) ]` .. but it is apparently skipping the first codon position in my hand while command `AlignmentToFilter[, -seq(3, ncol(AlignmentToFilter), by=3) ]` worked for me and omitted the 3rd codon position. ...
written 15 days ago by
al-ash • 0
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... For deleting 3rd codon position using R, see a related Q&A on biostars: [Reduce saturation by deleting the 3rd position in each codon of DNA seqs. R ape package][1]
[1]: https://www.biostars.org/p/132801/ ...
written 16 days ago by
al-ash • 0
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... I suggest to check [this article][1] on the benefits of MSA filtering for subsequent phylogeny reconstruction - you might decide not to filter at all after reading it :)
[1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538881/ ...
written 10 weeks ago by
al-ash • 0
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... Please note that by default the sequence header extracted by pyfaidx is truncated on first whitespace. ...
written 12 weeks ago by
al-ash • 0
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... I have the same question - does samtools faidx support regular expression/wildcards? (as I'm using samtools faidx in some of my previous scripts I'd prefer to stay with it rather than migrating to the python faidx) ...
written 12 weeks ago by
al-ash • 0
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... I'm using JSON API to retrieve from OrthoDB ortholog cluster ids for which genes are present in the selected species (e.g. Blatella germanica and Zootermopsis nevadensis), but apparently the retrieval is not limited with the argument `species=6973%2C136037` which I'm using; rather it retrieves all ...
written 6 months ago by
al-ash • 0
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... Note that it might be necessary to convert the *.sra to *.fastq using some special parametres supplied to `fastq-dump` to make it suitable for Trinity assembly (to take care of the read names), i.e. for paired reads:
SRA_TOOLKIT/fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files file.sra
...
written 7 months ago by
al-ash • 0
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... Ok, I did not realize that limiting the RAM might be because of not completely draining the machine - this makes sense. Thanks for clarification.
Since we touched this topic, I'm actually wondering - what if I set CPUs exceding the actual number of available CPUs? Would you expect some drop in tri ...
written 7 months ago by
al-ash • 0
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... Yes, but I'm not really sure whether it means, that the optimal performance will be reached when I set the max_memory as close to the expected peak RAM requirement as possible...I'm still wondering what effect will have if I set, for example, the max_memory much higher than required according to the ...
written 7 months ago by
al-ash • 0
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... I'm wondering if there is any guideline (or and advice from experienced user) on the `--CPU` and `--max_memory` parametres in Trinity (v2.3). Will suboptimal setting of these parametred dramatically influence the computational time?
E.g. I'm running assembly of 10M illumina paired reads (from insec ...
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