User: remi.b.md

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remi.b.md60
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Posts by remi.b.md

<prev • 11 results • page 1 of 2 • next >
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Answer: A: Fdist2 via Arlequin
... Facing similar issues, [Whitlock and Lotterhos 2014][1] have written their own implementation of Fdist2. It is available via [this Dryad repository][2]. It is not quite really user friendly but it comes with a R wrapper code that is nicely commented. [1]: http://onlinelibrary.wiley.com/doi/10.1 ...
written 2.4 years ago by remi.b.md60
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Fdist2 via Arlequin
... **Goal** I am trying to use the FDist2 methodology. [Lositan][1] seems to not be working anymore. [Arlequin](http://cmpg.unibe.ch/software/arlequin35/Arl35Downloads.html) has an implementation of FDist2, so I am now trying to use FDist2 via Arlequin via the command line. Note that I am on MAC OSX. ...
genome lositan selection snp arlequin written 2.4 years ago by remi.b.md60
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Comment: C: How to use Arlequin via the command line for FDist2?
... It is cross-posted indeed. Ok... I'll delete my post here (if I manage to find how) and may come back later depending on how the post goes on stackExchange. Thanks @WouterDeCoster for the feedback. ...
written 2.4 years ago by remi.b.md60
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Answer: A: How to indicate population structure in EggLib?
... There are two errors **First error** The function `make_structure` returns the Structure object but does not save it within `stats`. You therefore have to save this output. Structure = egglib.stats.make_structure(struct, None) **Second error** The Structure object must designate haploids. ...
written 2.8 years ago by remi.b.md60
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How to indicate population structure in EggLib?
... In Python, I am using [EggLib][1]. I am trying to calculate Jost's D value per SNP found in a VCF file. **Data** Data is [here](http://www.zoology.ubc.ca/~matthey/storage/) in VCF format. The data set is small, there are 2 populations, 100 individuals per population and 6 SNPs (all on chromosome 1 ...
vcf python egglib snp written 2.8 years ago by remi.b.md60
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Working example with pypgen
... I have a VCF file and which to calculate a few indices of population divergence over a sliding window. I consider using [pypgen][1] but the documentation is currently very limited. Can you please give me an example (for Jost'D for example) of a code that would work? [1]: https://pypi.python.org ...
pypgen vcf snp python written 2.8 years ago by remi.b.md60
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Comment: C: VCFtools installation and versions
... Indeed that's what raised my confusion. Also the fact that a version starting with a zero often mean that the produce is unfinished and not ready to be distributed contributed to my confusion. Thank you! ...
written 3.2 years ago by remi.b.md60
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VCFtools installation and versions
... I am trying to install vcftools on MAC OS X 10.11.3. I first installed it with homebrew brew install vcftools but when I do `man vcftools`, it appears the version that has been installed is `v0.1.13` while I was expecting the version 4.1 or something similar from what I could read online. So ...
vcf fst written 3.2 years ago by remi.b.md60 • updated 3.2 years ago by igor8.9k
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How to get the average number of pairwise differences among populations?
... I have genetic data in .structure and .vcf format (and can easily reach other formats with [PGDSpider][1]). The population of interest is structured and I would like to calculate the average number of pairwise differences (over a given window) between any pair of populations. Is there an existing t ...
genome software statistics written 3.4 years ago by remi.b.md60 • updated 3.4 years ago by Brice Sarver3.3k
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Answer: A: Trying to get a distribution of Exon lengths and Intron lengths.
... **Download data** In the terminal: curl ftp://ftp.ensembl.org/pub/release-84/gtf/gasterosteus_aculeatus/Gasterosteus_aculeatus.BROADS1.84.gtf.gz `curl` is for MAC OSX users. Use `wget` for Linux users. **Get Distributions** In R: library(GenomicFeatures) # This is a "BioConductor" pakc ...
written 3.5 years ago by remi.b.md60

Latest awards to remi.b.md

Scholar 2.4 years ago, created an answer that has been accepted. For A: How to indicate population structure in EggLib?
Scholar 2.8 years ago, created an answer that has been accepted. For A: How to indicate population structure in EggLib?
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Trying to get a distribution of Exon lengths and Intron lengths.

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