Tag: COG

I’m using the software plink2 (www.cog-genomics.org/plink/2.0/) and I’m trying to iterate over 3 variables. This software admits an input file with .ped extention file and an exclude file with .txt extention which contains a list of names to be excluded from the input file. The idea is to iterate over…

33.3.1.3 Oil Field Microbiology: Asia Oilfields in Russia and China have been extensively studied to determine microbial ecology as well as understand the microbial community for bioprospecting aspects. Molecular approaches as well as radioisotopic activity measurements from formation water of a high temperature oil reservoir in Russia (Samotlor) indicated enrichment…

Hi all, I have recently tried to estimate runs of homozygosity (ROH) from my vcf file by using plink 1.9. I ran following code to generate binary files that plink required: plink –vcf myfile.vcf –make-bed –out out_name –no-sex –no-parents –no-fid –no-pheno –allow-extra-chr This vcf file only contains one individual and…

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1. Szathmáry E, Smith JM. The major evolutionary transitions. Nature 1995;374:227–32. PubMed  Google Scholar  2. West SA, Fisher RM, Gardner A, Kiers ET. Major evolutionary transitions in individuality. Proc Natl Acad Sci USA. 2015;112:10112–9. CAS  PubMed  PubMed Central  Google Scholar  3. Moran NA. The coevolution of bacterial endosymbionts and phloem-feeding…

Cutoffs for Proxy Identification: D’ and R^2 0 I’m using a proxy-finding script with plink that reports potential proxies with their D’ and R^2: proxy D’ R^2 9:12345698:rs12345 1.0 0.000758121 9:12345999:rs87654 1.0 0.039958 9:12346999:rs54321 1.0 0.0399958 cf. www.cog-genomics.org/plink/2.0/ld However, what cutoffs should be used? From what I’ve read, D’ is…

Northumbria University is a member of the COVID-19 Genomics UK Consortium (COG-UK).  COG-UK is a pioneer in the use of large-scale, rapid whole-genome sequencing of SARS-CoV-2, the virus causing the COVID-19 pandemic, to understand viral transmission and evolution, and to inform public health responses and vaccine development. We seeking to…

Problem merging data in plink 1 welcome everybody… In short, this is the error message that appears: Error: 4 variants with 3+ alleles present. If you believe this is due to strand inconsistency, try –flip with merge-merge.missnp. (Warning: if this seems to work, strand errors involving SNPs with A/T or…

  linkage disequilibrium and haplotype analysis of GWAS . 0   Hi all, I have GWAS data. I have my data in 22 chromosome files in plink format. I have imputed genotype with Sanger imputation server. I use plink for my analysis but because plink 1.9 no more supports –hap…

Download COG Database 0 How to extract COG database for GAMMAPROTEOBACTERIA? database COG • 27 views Login before adding your answer. Source link

formatting error: Calculate LD matrix from bgen file 1 Hello, I am new to plink and am learning as I go. I am trying to calculate an LD matrix for a list of variants while using a bgen file as my reference population. See the command below: ./plink2/plink2 –r2 bin…