User: TimothéeFlutre

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Posts by TimothéeFlutre

<prev • 45 results • page 1 of 5 • next >
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Comment: C: does readVcf mistakenly ignore ploidy for missing genotypes?
... That would be great, thanks! ...
written 8 months ago by TimothéeFlutre70
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does readVcf mistakenly ignore ploidy for missing genotypes?
... Minimal reproducible example: library(VariantAnnotation) con <- url("https://raw.githubusercontent.com/timflutre/rutilstimflutre/master/inst/extdata/example.vcf") vcf.txt <- readLines(con) close(con) vcf.file <- "example.vcf" writeLines(vcf.txt, vcf.file) vcf <- readVcf(vcf.file) geno( ...
variantannotation readvcf gt missing written 8 months ago by TimothéeFlutre70
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Comment: C: error when plotting aligned reads depending on the length of the displayed regio
... I just sent you an email with a minimal reproducible example in attachment, thanks! ...
written 9 months ago by TimothéeFlutre70
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Comment: C: error when plotting aligned reads depending on the length of the displayed regio
... You're right, thanks. As I need to zoom in on a short sequence, I will also send an example data set to F. Hahne. ...
written 9 months ago by TimothéeFlutre70
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Comment: C: error when plotting aligned reads depending on the length of the displayed regio
... Thanks, I will try to do this next week. ...
written 9 months ago by TimothéeFlutre70
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error when plotting aligned reads depending on the length of the displayed region
... I would like to plot aligned reads from a bam file over a specific region. Everything works fine with the following command: alTrack <- AlignmentsTrack(my.bam.file, isPaired=TRUE) snp.pos <- 308632 plotTracks(alTrack, chromosome="chr1", from=snp.pos-200, to=snp.pos+100) But shortening the r ...
gviz plottracks alignmentstrack written 9 months ago by TimothéeFlutre70 • updated 9 months ago by hesham.gibriel0
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Add main title to ggbio's karyogram
... Hello, I would like to plot SNP coordinates (from a VCF file) along chromosomes using the ggbio package. But I can't succeed in adding the main title: library(VariantAnnotation) library(ggbio) fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation") vcf <- readVcf(fl, "hg19") aut ...
ggbio granges karyogram written 13 months ago by TimothéeFlutre70 • updated 13 months ago by Michael Lawrence9.8k
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extract subsequence(s) from DNAStringSet with getSeq
... I am writing a function which takes 2 inputs, a fasta file (with sequences) and a data.frame (with subsequence coordinates), and returning as output the given subsequences. Inside the function, the fasta file is loaded, the data.frame is converted into a GRanges, and the subsequences are extracted u ...
dnastringset getseq written 16 months ago by TimothéeFlutre70 • updated 16 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: different results between Rsamtools::pileup and samtools depth
... @Martin Morgan: thanks, I just sent you an email with a minimal, reproducible example. ...
written 18 months ago by TimothéeFlutre70
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Comment: C: different results between Rsamtools::pileup and samtools depth
... @Martin Morgan you're right, I'll look at a few differing positions and will post my solution (if I find one ;) ...
written 18 months ago by TimothéeFlutre70

Latest awards to TimothéeFlutre

Scholar 2.0 years ago, created an answer that has been accepted. For A: Write the "map" DataFrame from genotypeToSnpMatrix() to a text file

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