Moderator: Philipp Bayer
Philipp Bayer ♦ 6.7k
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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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... 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 5 weeks ago by
Philipp Bayer ♦ 6.7k
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... 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 7 weeks ago by
Philipp Bayer ♦ 6.7k
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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 7 weeks ago by
Philipp Bayer ♦ 6.7k
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... 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 6 months ago by
Philipp Bayer ♦ 6.7k
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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 6 months ago by
Philipp Bayer ♦ 6.7k
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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 7 months ago by
Philipp Bayer ♦ 6.7k
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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 7 months ago by
Philipp Bayer ♦ 6.7k
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... Amazing idea, I hadn't even thought of soft-clipping! I've currently written a relatively slow script that does what I describe in the OP post, after that I'll give BWA or similar a try, which is probably WAY faster, thanks for the idea!!
Edit: FWIW, here's the simple script I ended up using - ran ...
written 7 months ago by
Philipp Bayer ♦ 6.7k
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... (A few minutes later: Current best pipeline I can find is MAFFT/MUSCLE with gaps turned off, followed by trimAl, in a wrapper script to parallelise? curious to hear more!) ...
written 7 months ago by
Philipp Bayer ♦ 6.7k
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... I'm trying to automate the building of a reference database for DADA2. As such I'm using esearch to download ~200k fasta sequences for my search term of one gene from GenBank. Many GenBank sequences are joined-up sequences of several genes, and I'd like to trim those unnecessary genes away in order ...
written 7 months ago by
Philipp Bayer ♦ 6.7k
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