User: GabrielMontenegro

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Posts by GabrielMontenegro

<prev • 123 results • page 1 of 13 • next >
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Identifying mutations between haplotypes using haploNet (pegas) in R
... I think this might be an easy question, but I could not solve it after reading the pegas documentation. I want to plot an haplotype network using a FASTA file and identify which mutations are separatting the distinct haplotypes. **Example:** fa <- read.FASTA("example.fa") haps <- ha ...
haplotypes R pegas phylogenetics written 3 months ago by GabrielMontenegro400 • updated 21 days ago by Jie Ping20
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Comment: C: LD-decay in a r2 vs distance(cm) plot
... Could you give an example of those paper? ...
written 4 months ago by GabrielMontenegro400
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Answer: A: tools for Population branch statistics (PBS)
... Try ANGSD: http://www.popgen.dk/angsd/index.php/Pbs ...
written 5 months ago by GabrielMontenegro400
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Comment: C: What is population branch statistic (PBS)?
... If I remember correctly, they did simulations to estimate the power. I think they compared to Tajima's D or other commonly used selection statistics. You could check that section. But usually, FST-based methods will have good power to detect recent selection, because you can use a closely related po ...
written 5 months ago by GabrielMontenegro400
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Answer: A: What is population branch statistic (PBS)?
... If you'll go to the supplementary material you will find plenty of information regarding the statistic. It is a simple measure of distance between three populations (branch length T from Cavalli-Sforza, 1969) using FST. The PBS basically measures if there is an allele with extreme frequency compared ...
written 5 months ago by GabrielMontenegro400
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Comment: C: How to interpret XPEHH (recent selection) score?
... Isn't the sign of the XP-EHH score indicative whether the SNP is under selection in your tested or reference population? I thought (depending on how you computed XPEHH) you would only either positive or negative values. From the supp material: > An XP-EHH score is directional: a positive scor ...
written 8 months ago by GabrielMontenegro400
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Subsetting individuals in PLINK when IDs contain underscores "_"
... I am working with a VCF dataset and many individuals have IDs including an underscore. I want to subset them using plink, but I keep getting this error: Error: More than two instances of '_' in sample ID. Is there a way for plink to ignore the underscores in those IDs and treat them as a sing ...
plink written 9 months ago by GabrielMontenegro400 • updated 9 months ago by pfs250
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Comment: C: Forcing A1/A2 alleles in PLINK in a VCF phased file
... Thanks - that worked! ...
written 10 months ago by GabrielMontenegro400
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Comment: C: Forcing A1/A2 alleles in PLINK in a VCF phased file
... So then: `... --ref-allele force ancestral_snps.txt 1 2 ...`. Would this work? Thanks again. ...
written 10 months ago by GabrielMontenegro400
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Comment: C: Forcing A1/A2 alleles in PLINK in a VCF phased file
... So if I understand correctly, the `--ref-allele force` will make the specified (in this case ancestral) alleles be changed to 0? I am checking the help page, but I am not sure what this means: `{refcol} {IDcol} {skip}` ? What column numbers would I need to specify? Is it from the VCF or the `ancestr ...
written 10 months ago by GabrielMontenegro400

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