User: Francois Olivier Hébert

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280
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Quebec
Last seen:
8 years, 4 months ago
Joined:
9 years, 10 months ago
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f*******************************@ulaval.ca

Evolution, Bioinformatics, genetics, molecular ecology

Posts by Francois Olivier Hébert

<prev • 35 results • page 1 of 4 • next >
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Answer: A: How To Interpret Abyss Stats
... Well, in Simpson et al. 2009 (http://genome.cshlp.org/content/19/6/1117.full), the "sum" column is in Gbp, so my other guess would be that it is the total number of nucleotides (or bp). I'm not sure for which contig category though. It might only be for the n:N50 category. You could verify that by s ...
written 8.5 years ago by Francois Olivier Hébert280
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Comment: C: How To Interpret Abyss Stats
... Would it be possible that the "sum" column is the number of reads that were successfully assembled ? It would make sense, but I am not 100% sure though. But it's very probable. ...
written 8.5 years ago by Francois Olivier Hébert280
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Answer: A: How To Interpret Abyss Stats
... n:N50 is the number of contigs of at least N50 (which is "defined as the length N for which 50% of all bases in the sequences are in a sequence of length L < N" according to https://www.broad.harvard.edu/crd/wiki/index.php/N50) In the case of the "sum" column, I am not totally sure... this is am ...
written 8.5 years ago by Francois Olivier Hébert280
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Comment: C: How To Perform A Multilocus (Snp Genotype Data) Linkage Disequilibrium Analysis
... Thanks for the help! Actually, the problem with the input files for these tools is that information on chromosome and genetic distance is required... which I don't have. I'm working on the American whitefish for which the genome isn't sequenced yet. In fact, there is no salmonid genome currently ava ...
written 8.5 years ago by Francois Olivier Hébert280
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How To Perform A Multilocus (Snp Genotype Data) Linkage Disequilibrium Analysis Using R?
... Hi, I am working on a non-model species and I have a set of ~2300 genes in which I have identified multiple SNPs and I would like to perform a multilocus linkage disequilibrium analysis on my dataset. I've been looking on the web for a while now and I can't find anything that could help me with reg ...
R snp written 8.5 years ago by Francois Olivier Hébert280 • updated 8.5 years ago by Michael Dondrup48k
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Comment: C: Tool/Software That Predicts The Functional Impact Of Synonymous Mutations?
... Indeed, it was the wrong reference, I apologize for this. I know that people have focused a lot on transcriptional timing with regards to synonymous mutations and this is something that must be studied in the lab or with other tools than bioinformatics. But Kimchi-Sarfaty et al. (2007) seem to have ...
written 8.5 years ago by Francois Olivier Hébert280
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Comment: C: Tool/Software That Predicts The Functional Impact Of Synonymous Mutations?
... Thanks ! That's the impression that I had when I started looking in the literature. ...
written 8.5 years ago by Francois Olivier Hébert280
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Tool/Software That Predicts The Functional Impact Of Synonymous Mutations?
... Hi, I was wondering if anybody knows any program/application/tool that can be used to assess the functional impact of a SYNONYMOUS mutation on a given protein? I've used SIFT and PolyPhen-2 to measure the functional deleterious impact of non-synonymous mutations and I know that synonymous (silent) ...
mutation written 8.5 years ago by Francois Olivier Hébert280 • updated 6.1 years ago by Charles Warden8.0k
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Comment: C: Pgdspider - What Is The Format Of The "Population Definition" File - Vcf To Baye
... No I haven't found any direct solution to that problem with PGD Spider. Instead of trying to fix it, since I didn't have any answer, I created my own custom Python scripts to parse the VCF file, produce a genotype matrix file and then parse this genotype matrix file to create the input file for Baye ...
written 8.6 years ago by Francois Olivier Hébert280
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Dn/Ds Ratio - Paml : How Is It Possible To Obtain Negative Values For Dn Or Ds ?
... Hi, I have a set of 383 coding sequences in which there is a whole bunch of SNPs. I only have two species (2 populations representing incipient species). I used PAML to estimate the dn/ds ratio for each sequence. For some of the sequences, I get negative values either for dn, ds or dn/ds. I know ...
paml selection written 8.6 years ago by Francois Olivier Hébert280 • updated 8.5 years ago by Liam Thompson140

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