User: jamespoweraid2

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Posts by jamespoweraid2

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Comment: C: Plink: how to recode SNP identifiers
... I am sorry I mistakenly posted a comment as an answer and cannot delete it... ...
written 4.1 years ago by jamespoweraid20 • updated 7 weeks ago by RamRS25k
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Answer: A: Plink: how to recode SNP identifiers
... Thank you Christopher for your help! I realize Plink can do the recode of the alleles which is great, but can it also recode the SNP ID in file 1 so that they are similar format to the SNP IDs in file 2, i.e. only extracting the first part with rsIDs, and create BED/BIM/FAM file with the recoded SNP ...
written 4.1 years ago by jamespoweraid20 • updated 7 weeks ago by RamRS25k
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Plink: how to recode SNP identifiers
... Hi, I have two files I need to merge in Plink, but the SNP identifiers are different, i.e. file1 1       rs75454623:14930:A:G    0       14930   G       A 1       rs199856693:14933:G:A   0       14933   A       G file2 1       rs75454623:    0       14930   1       2 1       rs12354060      1 ...
plink input written 4.1 years ago by jamespoweraid20 • updated 4.1 years ago by christopher medway440
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Finding gene density from reference genome using R
... Hi, I was wondering if there is an easy way to find gene density (by counting the number of genes for example in a 10-Mbp window) in R across the whole genome?  Is this normally done by downloading the transcript data bed file? Thank you ...
R biomart written 4.2 years ago by jamespoweraid20 • updated 4.2 years ago by Giovanni M Dall'Olio26k
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Comment: C: Beagle files using the latest 1000 genomes
... Thank you very much Kamil! Would this get me the same files as if I ran the script here then? -- I am trying to get the `.filt.bgl.gz`, `filt.tabix.gz`, `.filt.markers` to be able to run EPIGWAS-- https://data.broadinstitute.org/srlab/BEAGLE/1kG-beagle-release3/READ_ME_beagle_phase1_v3 But using ...
written 4.2 years ago by jamespoweraid20 • updated 10 weeks ago by RamRS25k
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Beagle files using the latest 1000 genomes
... Hi, I would like to get the latest beagle files from vcf files from phase 3 of the 1000 genomes data with 2504 unrelated individuals that is here: http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/, which uses these 1000 Genomes vcf files: ftp://ftp.1000genomes.ebi.ac.uk/vol1 ...
1000genomes written 4.2 years ago by jamespoweraid20 • updated 4.2 years ago by Kamil2.0k

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