User: alexisdereeper

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4 years, 1 month ago
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Posts by alexisdereeper

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Get a table of minor an major allele from a vcf file
... You can use the SNiPlay web application that takes VCF files as input. http://sniplay.southgreen.fr/cgi-bin/home.cgi It generates a table with this kind of information... ...
written 4.1 years ago by alexisdereeper30
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Comment: C: Workflow Or Tutorial For Snp Calling?
... It should work with vcf4.2 format. Maybe there was a special caracter in the sample names that blocked the VCFtools program... ...
written 4.5 years ago by alexisdereeper30
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Answer: A: GWAS studies with RADSeq
... You can use SNiPlay that allows to manage VCF file and proposes methods for filtering, PCA, MDS plot, structure... http://sniplay.southgreen.fr/cgi-bin/analysis_v3.cgi ...
written 4.6 years ago by alexisdereeper30
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Answer: A: retrieval of population specific SNPs
... Hi! You can use SNiPlay for this purpose, that allows to assign individuals to groups/populations and then compare SNPs and help to define specific/shared SNPs... The Fst analysis (diversity analysis) allows to get SNPs that discriminates between 2 pop (Fst=1) http://sniplay.southgreen.fr/cgi-bin/an ...
written 4.6 years ago by alexisdereeper30
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Answer: A: How to calculate Hudson's Fst at Population and SNP level?
... Using a VCF file as input, SNiPlay implements VCFtools that calculates Fst (Weir and Cockerham’s) for each marker... http://sniplay.southgreen.fr/cgi-bin/analysis_v3.cgi ...
written 4.6 years ago by alexisdereeper30
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Answer: A: pull out flanking sequences of snp
... Do you have a VCF file listing all the SNPs in the reference? If so, you can use the SNiPlay application: http://sniplay.southgreen.fr/cgi-bin/analysis_v3.cgi Load your VCF file and select the plant genome used as reference. And then export flanking sequences of SNPs... ...
written 4.6 years ago by alexisdereeper30
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Answer: A: summarize SNPs and indels information in vcf file
... The SNiPlay online pipeline implements VCFtools and allows to summarize statistics information from VCF file: http://sniplay.southgreen.fr/cgi-bin/analysis_v3.cgi ...
written 4.7 years ago by alexisdereeper30
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Tool: SNiPlay3: a web application to analyze VCF files
... A new version of the web application SNiPlay is now available for analyzing VCF files online in different ways: filtering, comparing, population structure, haplotypes, annotation using SnpEff... SNiPlay3 is available here: http://sniplay.southgreen.fr/cgi-bin/analysis_v3.cgi Test it and report feedb ...
tool snp written 4.7 years ago by alexisdereeper30
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Answer: A: Obtain MAF from VCF
... The SNiPlay web application can report a tabular file including MAF information from a VCF file (using VCFtools): http://sniplay.southgreen.fr/cgi-bin/analysis_v3.cgi ...
written 4.7 years ago by alexisdereeper30
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Answer: A: minor allele frequency (MAF) from vcf
... The SNiPlay online pipeline implements VCFtools that calculates MAF from a VCF file: http://sniplay.southgreen.fr/cgi-bin/analysis_v3.cgi ...
written 4.7 years ago by alexisdereeper30

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