User: beausoleilmo

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beausoleilmo330
Reputation:
330
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Trusted
Location:
McGill University
Website:
http://marcolivierbeau...
Last seen:
1 month, 2 weeks ago
Joined:
4 years, 1 month ago
Email:
b***********@gmail.com

I'm a biologist using statistics and bioinformatics.

Having multiple interest in the world, I want to share what I learn with my entourage. If you have any questions or ideas to share with me, I’ll be glad to hear about it.

glimpse(Interests) :

Biology Ecology Scientific popularization Education Art Music Poetry Philosophy Programmation Politics Your ideas

Posts by beausoleilmo

<prev • 123 results • page 1 of 13 • next >
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Comment: C: Detect sex chromosomes from WGS on a bird species (with reference genome)
... Not really. I was hoping for a more “how to” solution since I’m not the most knowledgeable in this topic and that I’m not familiar with all the tools to do this. So I’m still looking. Wouldn’t it be cool to have a way to do that? ...
written 6 weeks ago by beausoleilmo330
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Comment: C: Error while creating .geno file with LEA
... Thanks for the follow up! ...
written 10 weeks ago by beausoleilmo330
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Comment: C: Error while creating .geno file with LEA
... I actually never got it to work... ...
written 12 weeks ago by beausoleilmo330
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Comment: C: Detect sex chromosomes from WGS on a bird species (with reference genome)
... I've never done that. I'm pretty sure there is a way to find the probability associated with aligning DNA strands to only sex chromosome of another species to find if the species would me homo or heterochromatic. I've just never seen anybody doing that. ...
written 6 months ago by beausoleilmo330
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Comment: C: Detect sex chromosomes from WGS on a bird species (with reference genome)
... The thing is that the reference genome doesn't have "chromosome" level data. Only scaffold. So the only way I see would be using LiftOver. But I'm wondering if there is something developed for that... ...
written 7 months ago by beausoleilmo330
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Detect sex chromosomes from WGS on a bird species (with reference genome)
... I'm wondering if there is a way to identify if there is a presence of sex chromosomes from WGS data. The reference genome is https://www.ncbi.nlm.nih.gov/genome/?term=txid48883[Organism:noexp] (it's a female https://www.ncbi.nlm.nih.gov/nuccore/AKZB00000000.1; female birds are heteromorphic (ZW)) an ...
wgs chromosomes written 7 months ago by beausoleilmo330 • updated 6 weeks ago by dalynoll0
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Answer: A: dxy (Nei 1987) calculation
... In [this paper][1], there is a link to [their supplementary material][2]. Within, these is a `genomescan_dxy.pl`. I'm not understanding Perl enough to be able to read and interpret what is happening, but that could be one way of doing it. [1]: https://genome.cshlp.org/content/25/11/1656.full. ...
written 7 months ago by beausoleilmo330
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Comment: C: ShapeIt giving Segfault 11?
... I'm trying to install SHAPEIT4 without any success on macOS Mojave... ...
written 7 months ago by beausoleilmo330
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Building a reference database for metabarcoding and obitools
... I'm generating a reference database for metabarcoding of diet to find trnL markers (so looking at plants only). I found the EMBL data that I was able to download using the following command wget -P $EMBL -nH --cut-dirs=5 -A rel_std_pln_*.dat.gz -m ftp://ftp.ebi.ac.uk/pub/databases/embl/releas ...
metabarcoding embl plants reference database diet written 7 months ago by beausoleilmo330
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Answer: A: Admixture - Abort trap: 6
... In my case, it was because the chromosome names, in the .bim file, were not supported by ADMIXTURE. # Make the first column a bunch of zeros. awk '{$1=0;print $0}' public.mm.bysubspecies.bim > public.mm.bysubspecies.bim.tmp # Rename the .bim file mv public.mm.bysubspecies.bim.t ...
written 7 months ago by beausoleilmo330

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Popular Question 4 months ago, created a question with more than 1,000 views. For File size on NCBI
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