User: michael.flower.14

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Posts by michael.flower.14

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Comment: C: Imputation from plink
... Thanks, I've updated above ...
written 6 months ago by michael.flower.140
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Imputation from plink
... I’ve got GWAS in plink format (bed, bim, fam). I need to impute some SNPs that weren’t directly genotyped. I’ve read that I need to phase, eg with shapeit, the impute, eg with impute2. I’m having trouble figuring out which genetic map to use for shapeit (the one on their guide doesn’t work). What wo ...
shapeit impute2 plink written 6 months ago by michael.flower.140
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Comment: C: Problems installing shapeit
... It’s 64 bit I believe. Can anyone help me run it on a Mac? https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html ...
written 6 months ago by michael.flower.140
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Comment: A: Problems installing shapeit
... I think the issue may be I have a mac running Catalina. Is there a way to run shapeit on mac?? ...
written 6 months ago by michael.flower.140
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Problems installing shapeit
... I've got GWAS data in plink format (.fam, .bed, .bim). I want to impute snps that weren't directly sequenced. I've read that IMPUTE2 is good. I gather I need to phase the data before. I've read SHAPEIT is good for that. I've downloaded it from here https://mathgen.stats.ox.ac.uk/genetics_software/sh ...
shapeit phasing written 6 months ago by michael.flower.140
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Comment: C: How to run pygraphviz on macOS in conda
... Done now I believe ... On 28 Aug 2019, at 16:00, RamRS on Biostar <mailer@biostars.org<a rel="nofollow" href="mailto:mailer@biostars.org">mailer@biostars.org> wrote: Activity on a post you are following on Biostarhttp://www.biostars.org User RamRSRamRS wrote Comment: How to run pygrap ...
written 9 months ago by michael.flower.140
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Comment: A: How to run pygraphviz on macOS in conda
... I’ve unticked all your comments now ... ...
written 9 months ago by michael.flower.140
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Comment: C: How to run pygraphviz on macOS in conda
... Think it's done now ... ...
written 9 months ago by michael.flower.140
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Comment: C: How to run pygraphviz on macOS in conda
... Thanks, I've done that ...
written 9 months ago by michael.flower.140
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Comment: C: How to run pygraphviz on macOS in conda
... Having said that, after removing the (?) damaged conda environment with your command `rm -rf /Users/michaelflower/miniconda3/envs/bioinfo`, I tried recreating the conda environment with `conda create -y --name bioinfo python=3.6`, and looks like it's all working. I've managed to run all the followin ...
written 9 months ago by michael.flower.140

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