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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Answer: A: RNA-seq analysis data analysis piepline
... I suggest the Hisat2/Stringtie/Ballgown pipeline, see Dave Tang's blogpost: https://davetang.org/muse/2017/10/25/getting-started-hisat-stringtie-ballgown/ For read cleaning and adapter trimming, have a look at fastp: https://github.com/OpenGene/fastp ...
written 10 days ago by Philipp Bayer5.9k
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Answer: A: how remove stopcodons from a GFF
... How are you running scipio? Looking at the manual, you run scipio with your amino acid fasta file, not your gff file: scipio.1.4.pl --blat_output=prot.vs.genome.psl genome.fa proteins.aa > scipio.yaml # takes ~7m In that case, your input amino acid file has stop codons, which are normall ...
written 14 days ago by Philipp Bayer5.9k
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Gff3 - moving an annotation from scaffold level to pseudomolecule level
... I have an annotation for a genome assembly in scaffold format in gff3/fasta format - someone else has ordered these scaffolds into pseudomolecules, so now I want to move the 'old' annotation in gff3 format from their scaffold positions into the pseudomolecules' position. I could write a script to ...
assembly annotation written 14 days ago by Philipp Bayer5.9k • updated 13 days ago by Carambakaracho760
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Comment: C: DESeq2 to do differential expression analysis for multiple groups
... If you really want to use time as the condition, yes it would be a bit like your table above - you'd have one table with time points A and B only, one table with time points A and C only, one with A and D, etc., B and C, B and D, etc. pp., Sure you can compare the first day with the other 6 days, ...
written 17 days ago by Philipp Bayer5.9k
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Answer: A: DESeq2 to do differential expression analysis for multiple groups
... I think what you're looking for is a time series analysis - there are some older biostars threads around this (for example https://www.biostars.org/p/125010/ ), here's a review paper which compares a bunch of MATLAB/R packages and finds that ImpulseDE2 works best for them: https://academic.oup.com/b ...
written 18 days ago by Philipp Bayer5.9k
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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 19 days ago by Philipp Bayer5.9k
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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 4 weeks ago by Philipp Bayer5.9k
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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 7 weeks 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 7 weeks 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 7 weeks ago by Philipp Bayer5.9k

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