User: beausoleilmo

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beausoleilmo300
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McGill University
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http://marcolivierbeau...
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17 hours ago
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3 years, 6 months ago
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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.

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

Posts by beausoleilmo

<prev • 119 results • page 1 of 12 • next >
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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 1 day ago by beausoleilmo300
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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 1 day ago by beausoleilmo300
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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 5 days ago by beausoleilmo300
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Comment: C: ShapeIt giving Segfault 11?
... I'm trying to install SHAPEIT4 without any success on macOS Mojave... ...
written 8 days ago by beausoleilmo300
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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 ...
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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 11 days ago by beausoleilmo300
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Comment: C: Sort VCF File by Position?
... Would there be an equivalent for a BCF? `bcftools view | [...]` code? Or why not using `bcftools sort -Oz output.bcf -o output_sort.vcf.gz`? ...
written 15 days ago by beausoleilmo300
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Comment: C: LD-decay in a r2 vs distance(cm) plot
... I ran something like that: vcftools --gzvcf output.bcf.flts.vcf.gz --plink --out output_in_plink1 plink --noweb --file output_in_plink1 --make-bed --out plinkedout plink --bfile plinkedout --extract plinkedout_thin.bim --recode --make-bed --out plinkedout_thin plink --bfile "plinke ...
written 21 days ago by beausoleilmo300
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Comment: C: Fast LD computation from VCF files using tomahawk
... I don't understand why but a lot of the flags in the tomahawk (version-0.7.0;) program are not working anymore. I've tried this tutorial and I had to change a lot of them. vcftools --gzvcf my.vcf.gz --recode --recode-INFO-all --thin 50000 --out "snp-thin" mv "snp-thin.recode.vcf" "snp-thi ...
written 21 days ago by beausoleilmo300
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Answer: A: How to parallelize bcftools mpileup with GNU parallel?
... I think that this would be a solution: I started with a file that contains the scaffold name and lengths: JH739887 30495534 JH739888 29527584 JH739889 22321128 [...] I then added a column with "1" in it to make it the "start" position. Since the scaffolds are not placed on the g ...
written 22 days ago by beausoleilmo300

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Popular Question 8 days ago, created a question with more than 1,000 views. For File size on NCBI
Great Question 11 weeks ago, created a question with more than 5,000 views. For How to order Admixture (ancestry) plot in R
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