Moderator: Philipp Bayer
Philipp Bayer ♦ 5.9k
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Post-Doc bioinformatics at the University of Western Australia, co-founder openSNP.org
Posts by Philipp Bayer
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... Not really, no - Kraken2 is so new that I haven't seen any benchmarks yet. Kraken1 was slower but more accurate (IIRC) ...
written 15 days ago by
Philipp Bayer ♦ 5.9k
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... Looks like you're looking for a metagenomics tool - tools like [Kraken 2][1] or [Centrifuge][2] are much faster for what you want to do
[1]: https://ccb.jhu.edu/software/kraken2/
[2]: https://ccb.jhu.edu/software/centrifuge/ ...
written 15 days ago by
Philipp Bayer ♦ 5.9k
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... Swiss-Prot is a manually curated database of proteins, available here: https://www.uniprot.org
Smith-Waterman is one of the more basic bioinformatics alignments for *local* sequence alignments, which is an optional setting in BLAST. Smith-Waterman is much more slower than BLAST's standard algorithm ...
written 19 days ago by
Philipp Bayer ♦ 5.9k
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... If I remember correctly, that column is reserved for phenotypes, which are not used in the PCA ...
written 5 weeks ago by
Philipp Bayer ♦ 5.9k
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... Could you maybe have used amigo**2**?
http://amigo2.geneontology.org/amigo/search/annotation
has 17,511 GO terms for *T. thermophila* ...
written 5 weeks ago by
Philipp Bayer ♦ 5.9k
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... You will probably get a better answer to your stats question on [Cross Validated][1]
[1]: https://stats.stackexchange.com/ ...
written 6 weeks ago by
Philipp Bayer ♦ 5.9k
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... Would [MultiQC][1] be fine? However, it makes a new HTML file summarising all input reports, I don't think it can make a CSV
[1]: https://multiqc.info/ ...
written 9 weeks ago by
Philipp Bayer ♦ 5.9k
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... The way I understand that thread, `sleuth_live`, **not** `sleuth` now has a single library running mode - `sleuth_live` is the web server for explanatory data analysis, it doesn't do differential expression ...
written 10 weeks ago by
Philipp Bayer ♦ 5.9k
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... Have you tried recompiling (rerunning install.sh)? Looks like ufasta is looking for GLIBC libraries that aren't there ...
written 10 weeks ago by
Philipp Bayer ♦ 5.9k
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... Thank you Kevin!
Yes, the coefficient makes much more sense - I'm using MVP currently which doesn't let me set `Major.allele.zero`, I will have to ask the authors! ...
written 11 weeks ago by
Philipp Bayer ♦ 5.9k
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