Moderator: Philipp Bayer

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Philipp Bayer5.9k
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PhilippBayer
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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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Comment: C: mapping unmapped reads to viral genome using blast+
... 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 Bayer5.9k
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Answer: A: mapping unmapped reads to viral genome using blast+
... 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 Bayer5.9k
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Answer: A: what is Swiss-Prot comparison?
... 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 Bayer5.9k
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Comment: C: EIGENSOFT: CONVERTF ignoring samples
... If I remember correctly, that column is reserved for phenotypes, which are not used in the PCA ...
written 5 weeks ago by Philipp Bayer5.9k
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Answer: A: geneontology.org GO annotations no longer present
... 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 Bayer5.9k
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Comment: C: Why use LASSO / elastic net in survival regression?
... 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 Bayer5.9k
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Answer: A: total beginner trying to learn about quality control
... 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 Bayer5.9k
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Comment: C: How to run sleuth in single run mode?
... 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 Bayer5.9k
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Comment: C: How to solve ufasta error while running MaSuRCA
... 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 Bayer5.9k
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Comment: C: FarmCPU - how to explain the reported 'effect'?
... 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 Bayer5.9k

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