User: Bioch'Ti

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Bioch'Ti1000
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France (Avignon)
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4 years, 10 months ago
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c******************@avignon.inra.fr

Posts by Bioch'Ti

<prev • 61 results • page 1 of 7 • next >
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Answer: A: Getting A Vcf File From A Fasta Alignment
... Hi, I also found that PGDSpider (http://www.cmpg.unibe.ch/software/PGDSpider/) is able to convert fasta alignment into a vcf file. The problem is that it does not handle concatened alignements in a single fasta file (eg sequences of different sizes). hope this helps Best, C. ...
written 5.0 years ago by Bioch'Ti1000
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Comment: C: Getting A Vcf File From A Fasta Alignment
... It will be nice to manage the indels too to make the script more general. But in my case, I do not need to consider these markers. ...
written 5.0 years ago by Bioch'Ti1000
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Comment: C: Getting A Vcf File From A Fasta Alignment
... The input file is a txt file (.fas for example) that contains only the aligned sequences (two lines per individual : one of comment, the second one for the sequence itself). Here is an example: >Ind1 ACGTGGCTAGATCA >Ind2 ACGTGGCTAGATCA >Ind3 ACGTGCCTAGATCA ...
written 5.0 years ago by Bioch'Ti1000 • updated 5.0 years ago by Pierre Lindenbaum116k
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Getting A Vcf File From A Fasta Alignment
... Hi All, I'm wondering if anybody is aware of a tool that converts a fasta alignment (that includes fasta sequences of different individuals) into a vcf file? I know that the opposite is feasible (vcf to fasta) using the GATK dedicated tool, but I want to perform the opposite ! Thanks for your hel ...
vcf fasta alignment conversion written 5.0 years ago by Bioch'Ti1000
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What Are The Softwares To Infer The Derived Or Ancestral State Of Polymorphic Sites ?
... Hi, I'm looking for a method/software to infer the ancestral or derived state of polymorphic sites using DNA alignments (in fasta format). For example, I have already identified thousands of orthologs between three plant species and aligned them (one species and two outgroups). Now, I would like to ...
plant allele written 5.2 years ago by Bioch'Ti1000 • updated 5.2 years ago by Joseph Hughes2.7k
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Answer: A: Dmr (Differentially Methylated Regions) Identification Software
... Hi, Maybe you could start with reading this review paper: Analysing and interpreting DNA methylation data : http://www.nature.com/nrg/journal/v13/n10/full/nrg3273.html Best ...
written 5.2 years ago by Bioch'Ti1000
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Answer: A: Is Igv Software The Only Available Software To Open Bam File
... Hi, you can also check Consed here : http://www.phrap.org/consed/consed.html Have Fun ...
written 5.3 years ago by Bioch'Ti1000
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Comment: C: Volcano Plot Of Significantly Differential Exp Genes
... From a biological point of view, I'm wondering what is the interpretation of such a volcano plot? I mean, I find 'suspicious' that the DE genes show very low fold changes... (even on a log2 scale). Do you expect such pattern? ...
written 5.3 years ago by Bioch'Ti1000
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Answer: A: Reliable Tools To Filter Vcf Format Files
... Hi, You can also look at the extension of Plink! that manages VCF files: http://atgu.mgh.harvard.edu/plinkseq/overview.shtml Best ...
written 5.4 years ago by Bioch'Ti1000
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Answer: A: Gwas With Covariates From Principle Component Analysis
... Hi, If your association panel is not structured (your PCA results should tell you), then only the kinship matrix (K) should be included in the GLM/MLM model to perform the GWA. Otherwise, you have to take into account the population structure as covariate whatever the method you used to evaluate the ...
written 5.4 years ago by Bioch'Ti1000

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