User: Davide Chicco

gravatar for Davide Chicco
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Canada
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http://www.davidechicc...
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1 month, 2 weeks ago
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7 years, 4 months ago
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Posts by Davide Chicco

<prev • 29 results • page 1 of 3 • next >
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Comment: C: bcftools / samtools, which database does the MAF function use?
... Hi Pierre Thanks for the reply. Are you saying the information about if a variant is rare (or not) is present in the header of the VCF file we're using? If yes, how does bcftools view retrieve it? And, more important, how can we know which database did the people who generated the file used to st ...
written 7 weeks ago by Davide Chicco80
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bcftools / samtools, which database does the MAF function use?
... Hi I am working with `bcftools view` to [filter variants][1] based on a specific MAF (minor allele frequency) cutoff. It works well but there's an information I am missing: which database is bcftools using to apply the MAF filter, that is to claim if a variant is rare or not? Thanks! -- Davide ...
maf bcftools samtools written 7 weeks ago by Davide Chicco80 • updated 7 weeks ago by Pierre Lindenbaum120k
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Comment: C: How to check the presence of mutations of a specific gene in a specific VCF file
... Hi Erin_Ensembl another question: I am exploring VEP; how are non-synonymous variants labeled in a typical VEP output? I see many biotypes (nonsense_mediated_decay, protein_coding, retained_intron, etc) but I cannot understand if one is suitable for me. Thanks! ...
written 11 weeks ago by Davide Chicco80
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Comment: C: How to check the presence of mutations of a specific gene in a specific VCF file
... Hi Erin_Ensembl Thanks for your reply, very useful. Unfortunately, I don't have that information in the variants of my VCF files. I plan to use [SnpEff][1] to annotate it. To select the non-synonymous variants, should I filter only the "missense_variant" variants then? Or something more? [1]: ...
written 11 weeks ago by Davide Chicco80
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bash, how can I distinguish synonymous from non-synonymous variants in VCF files?
... My goal was to find the variants related to a specific gene in a VCF file, through bash in a terminal shell. The wonderful BioStars community helped me understand that in a [previous discussion][1]. For example, to detect the variants of the ARIH1 gene in the inputFile.vcf.gz file, I can run the fo ...
vcf R variant written 11 weeks ago by Davide Chicco80 • updated 11 weeks ago by karl.stamm3.5k
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Comment: C: How to check the presence of mutations of a specific gene in a specific VCF file
... Hi Erin_Ensembl and finswimmer Thanks for your help. I have another question for you. Among the variants that I select in my VCF files through the `bcftools view` command, I need to choose only the **non-synonymous variants**. Do you know how I can modify my `bcftools view` accordingly? Or what b ...
written 11 weeks ago by Davide Chicco80
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Bioconductor, how to convert an ExpressionFeatureSet to an ExpressionSet?
... I am performing a batch correction with Bioconductor. For the files in the same batch, I use the function [rma()][1] to normalize the data. This function calls return `ExpressionSet` objects that I combine all together into a unique vector. When I have a batch containing only one file, I cannot ru ...
bioconductor written 11 weeks ago by Davide Chicco80
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Problems with ArrayExpress datasets downloads on Bioconductor
... Hi all I need to download 3 datasets from ArrayExpress: [E-MTAB-5273][1], [E-MTAB-5274][2], and [E-MTAB-4451][3]. I tried to do that in R by using the [ArrayExpress() function][4] of the [ArrayExpress package][5] on Bioconductor, but it generate errors for all the three cases. I am using R version ...
arrayexpress bioconductor written 12 weeks ago by Davide Chicco80 • updated 7 weeks ago by h.moosavi570
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Datasets of genomic regions related to heart failure?
... Hi I am looking for datasets of genomic regions (in the format: chromosome number, starting locus, ending locus) of variants of genes related to heart failure. Does anyone know where I can find some? I am looking for something like the [VISTA Enhancer Browser][1], but related to heart. That websi ...
dataset heart written 12 weeks ago by Davide Chicco80
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Comment: C: How to check the presence of mutations of a specific gene in a specific VCF file
... Hi [finswimmer][1] and [Erin_Ensembl][2], Thanks for your help, all very clear. Using VEP might be an option for the future, but unfortunately not for now because for patients' privacy reasons I cannot upload VCF files anywhere. Thanks again! :-) [1]: https://www.biostars.org/u/37605/ [2]: h ...
written 3 months ago by Davide Chicco80

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