User: willgilks

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willgilks230
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230
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Trusted
Location:
United Kingdom
Website:
https://zenodo.org/com...
Twitter:
@wpgilks
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Last seen:
4 months, 3 weeks ago
Joined:
2 years, 10 months ago
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Post-doc at Sussex Uni, UK. Looking for a job.

 

Posts by willgilks

<prev • 33 results • page 1 of 4 • next >
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Window and step size for LD-independent SNPs
... Hi, I'm trying to determine which of my SNPs from WG-NGS are independent of LD, i.e. tagging SNPs. The downstream use for this is when testing genotypes against a trait, the number of independent tests is known, generally allowing significance thresholds to be set. I've tried different window size ...
plink ld snp r2 written 5 months ago by willgilks230
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Answer: A: Subsetting individuals with Plink. Error: Line 1 of --keep file has fewer tokens
... from https://www.cog-genomics.org/plink/1.9/filter > --keep accepts a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column, and removes > all unlisted samples from the current analysis. So like this: HG00096 HG00096 HG00097 HG0 ...
written 6 months ago by willgilks230
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Answer: A: Load BED file on UCSC
... You don't need the quotation marks. ...
written 8 months ago by willgilks230
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Answer: A: Best visual and interactive genotype matrix (VCF) exploration tool
... I've found the Integrated Genomics Viewer pretty good http://software.broadinstitute.org/software/igv/. It displays vcf files, with variants coloured by genotype and good zoom and scroll functions .. limited for very big files. Also you can view bam and gwas data with it. ![enter image description ...
written 8 months ago by willgilks230
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Answer: A: Genetic measures calculation in vcf files
... Hi Ricardo, I think you're getting values of NaN because you are only analysing one individual. Population genetics requires more than one individual, of course. Combine the separate vcf files from each individual into one, then analyse. GATK is good for this function http://gatkforums.broadinsti ...
written 9 months ago by willgilks230
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Answer: A: How to conduct pathway analysis from VCF file?
... RNA seq quantifies the expression level of each individual gene. Exome sequencing does not. Therefore it is not possible to do pathway analysis of expression levels from exome sequencing data. ...
written 9 months ago by willgilks230
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Answer: A: How to overlay qq plots
... I've run the code for the two answers above, and the plots do not look the same, because the R qqplot function applies a transformation to the data. The code on this page generates a qqplot like the one in the example, although it's using lattice, not ggplot http://genome.sph.umich.edu/wiki/Code_Sa ...
written 9 months ago by willgilks230
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Answer: A: How to conduct pathway analysis from VCF file?
... Hi David, Your question seems a bit strange. You have genotype data, and now you want to find out which proteins interact .. and you want to apply a pathway analysis but don't know what to apply it on. Perhaps, the missing step in your plan is to calculate which genetic variants are correlated wit ...
written 9 months ago by willgilks230
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Answer: A: How to predict amino acid sequence after a framshift deletion in the gene
... Hi Inayat, I've posted a few links to translation tools below. Get one nucleotide sequence for the full-length open-reading-frame without the deletion, and one with the deletion, preferably in fasta format. Put them both through the translate-tool. Ensure that you have the correct, in-frame start c ...
written 9 months ago by willgilks230
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Answer: A: Problems with converting data
... Hi Roymand, I'd tenatively call that a genotype matrix, and say that it's in dosage format, in that the value in each cell indicate how many copies of the alternate allele each individual has. Plink 1.9 can read dosage format files as described here https://www.cog-genomics.org/plink2/assoc#dosage ...
written 9 months ago by willgilks230

Latest awards to willgilks

Scholar 9 months ago, created an answer that has been accepted. For A: Genomestrip Generate Haploid CNV Genotypes
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Box plot using ggplot2
Scholar 9 months ago, created an answer that has been accepted. For A: Genomestrip Generate Haploid CNV Genotypes
Scholar 18 months ago, created an answer that has been accepted. For A: Genomestrip Generate Haploid CNV Genotypes

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