Moderator: Philipp Bayer

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Philipp Bayer6.0k
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PhilippBayer
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6 years, 11 months ago
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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: Google Summer of Code and Open Bioinformatics Foundation is looking for students
... Hi Eshwari! I'm afraid this post is 3 years old, our GSoC project ended a long time ago! However, this round of GSoC will be announced in 3 weeks: https://summerofcode.withgoogle.com/?csw=1 I'm sure there'll be many bioinformatics projects again this year, good luck!! ...
written 6 weeks ago by Philipp Bayer6.0k
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Comment: C: What's the right way to submit a genome assembly to NCBI?
... As an aside, if you're with an Australian institution you can use EMBL-ABR's data chaperoning service, they will do this work for you : https://www.embl-abr.org.au/data-chaperoning/ ...
written 8 weeks ago by Philipp Bayer6.0k
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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 10 weeks ago by Philipp Bayer6.0k
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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 10 weeks ago by Philipp Bayer6.0k
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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 11 weeks ago by Philipp Bayer6.0k
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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 3 months ago by Philipp Bayer6.0k
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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 3 months ago by Philipp Bayer6.0k
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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 3 months ago by Philipp Bayer6.0k
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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 4 months ago by Philipp Bayer6.0k
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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 4 months ago by Philipp Bayer6.0k

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