User: felipead66

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felipead6630
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Posts by felipead66

<prev • 24 results • page 1 of 3 • next >
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Linkage disequilibrium from multi-sample vcf file
... I have a multi-sample vcf file annotated with snpeff. I want to calculate the linkage disequilibrium. I have 2 questions: 1. I use vcftools, in particular `./vcftools --vcf input_vcf.vcf --geno-r2 --out output` and it takes forever (it runs a week and keeps on). Is this OK? 2. Is it appropria ...
vcf snpeff vcftools ld written 10 weeks ago by felipead6630 • updated 10 weeks ago by RamRS23k
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fasta sequences from snpeff output file
... Is it possible to extract the fasta sequences of specific genes from a snpeff output (vcf) file? ...
fasta snpeff written 12 weeks ago by felipead6630
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Comment: C: Chromosomal length prunus dulcis
... Thank you for your reply, I followed the instructions in the link and I would not trust it since I get around 10000 (!) chromosomes. So there must be something else, I do not know what went wrong. ...
written 12 weeks ago by felipead6630
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Chromosomal length prunus dulcis
... Is it possible to find the chromosomal length of prunus dulcis? https://www.rosaceae.org/organism/Prunus/dulcis I want to use it to build circus plots. ...
length non-model chromosomes written 12 weeks ago by felipead6630 • updated 12 weeks ago by SMK1.8k
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Comment: C: snpEff output gets zero results for synonymous SNPs
... Thank you very much, that is every helpful. But, still, how do I get the non_synonymous? Furthermore, I assume that the synonymous_variant are in the coding region? ...
written 3 months ago by felipead6630
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Comment: C: snpEff output gets zero results for synonymous SNPs
... You mean the command line to create the snpEffoutput.vcf file? ...
written 3 months ago by felipead6630
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Comment: C: snpEff output gets zero results for synonymous SNPs
... Yes, this gives me 81949 results. But again, when I do `grep -c 'non_synonymous' snpEffoutput.vcf I` still get 0 results. ...
written 3 months ago by felipead6630 • updated 3 months ago by finswimmer12k
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snpEff output gets zero results for synonymous SNPs
... I have a vcf file after using snpEff annotation. I want to extract information from this file so I search for synonymous (and non-synonymous) sites. But when I do grep -c "SYNONYMOUS" snpEffoutput.vcf I get 0 results. Does this mean there is something wrong with my file? ...
snpeff synonymous written 3 months ago by felipead6630 • updated 3 months ago by finswimmer12k
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Comment: C: In which step should plink be used?
... typo, the correct is "snp identification" ...
written 3 months ago by felipead6630
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In which step should plink be used?
... I have read some papers that use plink in their studies for snps. I also have read plinks' documentation. I have not, though, figured out WHEN to use the plink in the process for snp identification. Could you please give some advice on when to use plink? ...
snps plink written 3 months ago by felipead6630 • updated 3 months ago by WouterDeCoster40k

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