User: Johan Zicola

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Johan Zicola60
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Posts by Johan Zicola

<prev • 13 results • page 1 of 2 • next >
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Answer: A: 'gene_name' is missing in StringTie output file 't_data.ctab'
... The problem may come from the fact that you are using non-human data. I am working with Arabidopsis and I also noticed the empty field for `gene_name` column in `t_data.ctab` file from StringTie. I thought it was a bug but if you look at this [Ballgown documentation](https://www.bioconductor.org/pac ...
written 7 months ago by Johan Zicola60
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Answer: A: Heterozygosity by individual
... VCFtools has the function `--het` such as `vcftools --vcf input.vcf --het --out output.het` > --het > Calculates a measure of heterozygosity on a per-individual basis. Specfically, the inbreeding coefficient, F, is estimated for each individual using a method of moments. The resulting file ha ...
written 16 months ago by Johan Zicola60
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Answer: A: Why main diagonal of gemma relatedness matrix is not equal to 1
... I've got the answer from the creator of GEMMA Xiang Zhou: > The centered relatedness matrix does not scale each column of the genotype matrix, so the main diagonal of the resulting relatedness matrix will not be close to 1s (usually around 0.3 depending on maf etc.). If you use the scaled relat ...
written 20 months ago by Johan Zicola60
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Answer: A: How To Find The Locations Of A Short Specific Sequence In A Genome With 1 Or 2 M
... Using **Bowtie** (for example v1.2.2 here) to find off-targets for defined CRISPR-Cas9 target sequences: Make the Bowtie index for your genome (fasta file format) bowtie-build -f genome.fa genome_prefix Search for your target sequence by allowing 1 mismatch (for your N) with the flag `-n 1` ...
written 2.0 years ago by Johan Zicola60
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Answer: A: How to identify which SNPs in my dataset are genome wide significant
... It seems your QQplot and Manhattan plot were generated with the R package [qqman](https://github.com/stephenturner/qqman). You can filter out the SNPs above the threshold you define, the blue and red lines being set by default at -log10(1E-5) and -log10(5E-8) (check [documentation](https://cran.r-pr ...
written 2.2 years ago by Johan Zicola60
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Comment: C: Why main diagonal of gemma relatedness matrix is not equal to 1
... I thought the terms kinship matrix and relatedness matrix could be used interchangeably. Gemma documentation should be updated to use the accurate term. I understood that a value >0.5 (self-kinship) or >1 (self-relatedness) could be explained by consanguinity but I still don't understand why I ...
written 2.2 years ago by Johan Zicola60
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Comment: C: Why main diagonal of gemma relatedness matrix is not equal to 1
... Thanks for your comment. Looking around, I could find that usually the main diagonal is made of 1 or values above 1 if consanguinity. The figure 1 of the [Bae et al 2014][1] is illustrating well what I expect from a kinship matrix. Since individuals compared to themselves are based on the same SNP c ...
written 2.4 years ago by Johan Zicola60
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Why main diagonal of gemma relatedness matrix is not equal to 1
... I am running GWAS analyses with gemma that seem to work but when I open the centered relatedness matrix (.cXX), I do get a symmetric matrix but the main diagonal is not made of 1s ... why? The [manual][1] p.11 part 3.3.1 shows an example of matrix with a main diagonal which is not made of 1s. I al ...
gwas relatedness matrix kinship matrix gemma written 2.4 years ago by Johan Zicola60
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Comment: C: How to extract specific chromosome from vcf file
... This won't work, separating chromosome names by commas neither (though it works for `bcftools view --regions 1,2,3`). Do rather `vcftools --gzvcf --chr 1 --chr 2 [ etc. until 23] --recode --out subset_chr1-23` ...
written 2.5 years ago by Johan Zicola60
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Comment: C: How to extract specific chromosome from vcf file
... Note that this method is better than grep as it includes the VCF header. However, it won't change the header of the VCF file so the unselected chromosomes will still have their ID line, e.g *##contig=*. So don't rely on `bcftools view -h subset.vcf` to verify what chromosomes are left in your VCF fi ...
written 2.5 years ago by Johan Zicola60

Latest awards to Johan Zicola

Voter 9 months ago, voted more than 100 times.
Popular Question 13 months ago, created a question with more than 1,000 views. For Why main diagonal of gemma relatedness matrix is not equal to 1
Scholar 20 months ago, created an answer that has been accepted. For A: Why main diagonal of gemma relatedness matrix is not equal to 1
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Does vcf-consensus support indels?
Supporter 2.4 years ago, voted at least 25 times.

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