Moderator: Zev.Kronenberg

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https://eichlerlab.gs....
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zevkronenberg
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Postdoc in the Eichler lab.  Studying structural variant and its role in disease and human evolution.

Posts by Zev.Kronenberg

<prev • 954 results • page 1 of 96 • next >
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Answer: A: how to run STRUCTURE command n times for each K value?
... Since perl is still cool. Here's the gist, perl -e 'print join "\n", (0..10)' | xargs -I {} -P 10 admixture -K {} -o {}.something ...
written 1 day ago by Zev.Kronenberg10k
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Comment: C: Multiple hypothesis testing, Fst outliers
... It really depends on the study. In the case of the Ephb2 (head crest), the allele was recessive so we were able to reach significance. If i remember correctly, pFst withstood a multiple test correction. ...
written 3 months ago by Zev.Kronenberg10k
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Answer: A: metagenomic profiling and population analysis
... Here's a paper out of my old lab: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0969-1 ...
written 3 months ago by Zev.Kronenberg10k
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building all possible phylogenies.
... Given a starting phylogeny, something like: (susie_ggo,(clint_ptr,(yri_hsa,chm13_hsa)),susie_pab); Is there a tool to generate all other possible trees? i.e: (susie_ggo,(clint_ptr,(yri_hsa,chm13_hsa)),susie_pab); (clint_ptr,(susie_ggo,(yri_hsa,chm13_hsa)),susie_pab); (susie_ggo,( ...
phylogenetics written 3 months ago by Zev.Kronenberg10k • updated 3 months ago by h.mon7.5k
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Answer: A: Multiple hypothesis testing, Fst outliers
... Chris, I'm happy to hear people are using GPAT code within VCFLIB. While unpublished, there is a working manuscript in the VCF github. I've tried to describe, in better detail, what pFst and other GPAT tools do. pFst is terribly named (i don't take responsibility), because it is a likelihood ra ...
written 4 months ago by Zev.Kronenberg10k
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Comment: C: Fasta File To Sam Conversion
... https://www.biostars.org/u/2/ and yet here I am looking for a solution. Also large sequencing centers are now delivering unaligned bam files. It's not sane, but so it goes. ...
written 4 months ago by Zev.Kronenberg10k
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Comment: C: remove gapped bases in MSA
... " -nogaps " is the flag. thanks. ...
written 6 months ago by Zev.Kronenberg10k
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remove gapped bases in MSA
... I have a multiple sequence alignment represented as a "mulit-fasta." I want to remove any column that contains a gap. Thought I would ask before writing my own. ...
alignment msa written 6 months ago by Zev.Kronenberg10k • updated 6 months ago by abascalfederico960
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Comment: C: Estimating FST per genome
... You can only calculate FST for segregating sites. if(populationTarget->af == -1 || populationBackground->af == -1){ delete populationTarget; delete populationBackground; continue; } if(populationTarget->af == 1 && populationBackground->af == 1){ delete popu ...
written 7 months ago by Zev.Kronenberg10k
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Answer: A: Estimating FST per genome
... For a genomic average I would just use Weir and Cockerham's FST (1984) for each site then build a distribution across the genome. You can also just take the average across the site FST values. I've implemented this method in VCFLIB. If you're interested in learning more about FST I've tried to n ...
written 7 months ago by Zev.Kronenberg10k

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