Moderator: Philipp Bayer

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Philipp Bayer6.8k
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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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Merging and then unmerging small contigs
... We've been using mosdepth a lot for coverage calculation of plant pangenomes but it starts to choke when you have many, many tiny contigs instead of a few large chromosomes because of the way the algorithm works. I'm wondering - is there any tool which can take bam files of reads aligned to those c ...
bedtools mosdepth written 11 days ago by Philipp Bayer6.8k
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Answer: A: Things you wish you knew when entering the bioinformatics field
... As a bioinformatician you have a (currently) very valuable skill-sets. People will seek you out, hoping that you'll do their analysis for them. I have been burned by this because people don't know what you can and cannot do, so they come to you with insufficient data, with a vaguely defined biologic ...
written 8 weeks ago by Philipp Bayer6.8k
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Comment: C: Braker output into maker (Annotation)
... This would be its own good question but yeah, right now I lean towards not running RepeatMasker via MAKER, but instead later remove proteins tha tare X% covered by known repeats or contain transposase related domains ...
written 9 weeks ago by Philipp Bayer6.8k
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Comment: C: Error in Calculation of Ka/Ks value using Ka/Ks calculator
... I edited your comment to make the code look nicer, I don't know perl much, but isn't your input already a clustalw alignment? I don't understand what your input file is, there are many ways to store an orthologous gene family? ...
written 4 months ago by Philipp Bayer6.8k
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Comment: C: Multiple Sequence Alignment for Full length genomes
... Another option: Rob Lanfear has a repo up where he has already run the MSA https://github.com/roblanf/sarscov2phylo/ He uses MAFFT too in this script https://github.com/roblanf/sarscov2phylo/blob/master/scripts/global_profile_alignment.sh ...
written 5 months ago by Philipp Bayer6.8k
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Answer: A: KaryoploteR for copy number
... I think you switched up your variables, custom.genome needs the actual chromosome lengths and no other measurements, the table you have there needs to be given to kpPlotDensity(), not to plotKarytyope() Have a look at this code I wrote a while ago which uses custom.genome too: https://github.com/ph ...
written 5 months ago by Philipp Bayer6.8k
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Answer: A: Getting assembly from sam/bam file
... I think it's probably best if you use RaGOO for that - https://github.com/malonge/RaGOO It runs minimap2 using your contigs and a reference assembly and then orders the contigs based on the alignment. You may have to rerun your alignments, I don't know whether you can give it the sam file directly. ...
written 9 months ago by Philipp Bayer6.8k
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Comment: C: PLINK --allow-extra-chr error
... Have you tried using --allow-extra-chr without the 0? Have you tried looking at line 938485, 938486, 938487 to see whether these lines are just broken somehow? ...
written 10 months ago by Philipp Bayer6.8k
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Comment: C: Brassica napus reference genome
... Hi, here's a different fixed version: https://cloudstor.aarnet.edu.au/plus/s/hPwZU13L1Hx2nFM I re-added the missing gene-lines and sorted by chromosome and position ...
written 11 months ago by Philipp Bayer6.8k
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Comment: C: Brassica napus reference genome
... Hmmmm can't find it myself any more :O I got it on an old laptop? I'll re-create the file asap ...
written 11 months ago by Philipp Bayer6.8k

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