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User: Johan Zicola

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Johan Zicola • 50
Reputation:
50
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New User
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Last seen:
1 week, 6 days ago
Joined:
1 year, 10 months ago
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i******@hotmail.fr

Posts by Johan Zicola

<prev • 11 results • page 1 of 2 • next >
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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 13 days ago by Johan Zicola • 50
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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 5 months ago by Johan Zicola • 50
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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 6 months ago by Johan Zicola • 50
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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 7 months ago by Johan Zicola • 50
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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 9 months ago by Johan Zicola • 50
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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 9 months ago by Johan Zicola • 50
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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 10 months ago by Johan Zicola • 50
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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 10 months ago by Johan Zicola • 50
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Answer: A: Generating random DNA sequence and paired-end alignment
... I wrote a python script with the different functions you would need to test structural variation calling on either randomly generated fastq files or fastq files generated based on a given specified fasta file. Find the script and documentation on https://github.com/johanzi/fastq_generator ...
written 11 months ago by Johan Zicola • 50
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Answer: A: Does vcf-consensus support indels?
... Not sure about vcftools-consensus but indels are taken into account with "bcftools consensus" and is probably faster than vcftools: bcftools consensus --fasta-ref --sample -o See docs: https://samtools.github.io/bcftools/bcftools.html ...
written 14 months ago by Johan Zicola • 50

Latest awards to Johan Zicola

Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Does vcf-consensus support indels?
Supporter 9 months ago, voted at least 25 times.
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