User: rc16955

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rc1695550
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Posts by rc16955

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Count variants between two samples within a multi-sample VCF
... Sorry to double post. You seem familiar with BioAlcidaeJdk, do you think it could be used for the next step in my analysis? I'd like to be able to see where in the genome variants within pairwise comparisons are falling. Would it be possible, using BioAlcidaeJdk, to get a list of each genomic positi ...
written 3 months ago by rc1695550
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Comment: C: Count variants between two samples within a multi-sample VCF
... Thanks very much for the suggestion, I have given it a try and it seems to work well! Can I just confirm that the number output for each pair is the number of positions where the two samples undergoing comparison have *the same* genotype, so that more similar samples have *higher* numbers in the ou ...
written 3 months ago by rc1695550
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Count variants between two samples within a multi-sample VCF
... Hi all, I have a vcf file containing variant data for 52 samples. - sample 1 - sample 2 - sample 3 - etc., etc. What I would like to do is perform pairwise comparisons where I count the number of variants (SNPs and small INDELs) between each sample and each other sample. - number of variant ...
vcf vcftools written 3 months ago by rc1695550 • updated 3 months ago by chrchang5234.8k
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(Closed) Make bed files for different functional group given GFF3 file
... Hi! I am trying out something new and am already a little stuck. Any assistance would be really appreciated. I have whole genome sequencing data for a number of samples, which I have already mapped to the reference assembly for my study species. These are currently in sorted bam files. I would now ...
gff alignment annotations exon functional groups written 4 months ago by rc1695550
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Best program for population structure analyses of whole genome SNP data of many individuals
... Hello and thanks for reading, I am investigating the population genetic structuring of my study species using whole genome SNP data, and would like suggestions for software that can assign individuals to genetic clusters within my samples. It would also be useful to calculate fixation indeces betwe ...
genome software population sequencing written 8 months ago by rc1695550
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Opening VCFTools Linkage output in HaploView
... Hello all, I have some linkage data obtained with VCFTools, based on a VCF file that was in turn generated from a bunch of bam files each corresponding to the complete genome sequence of an individual of my study species. The command used to generate the linkage data was this: vcftools --vcf ...
linkage next-gen vcftools haploview sequencing written 2.0 years ago by rc1695550
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Branch Lengths in RAxML
... Hi all, I know that this is an elementary question, but it's one that I've been struggling to find the answer to. When RAxML calculates branch lengths on default settings, what exactly do the numbers it produces mean? I gather that it's a measure of genetic distance between two nodes, but how is ...
phylogeny raxml written 2.3 years ago by rc1695550 • updated 2.0 years ago by lay_050
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Meaning of "Cannot allocate [number] character vector" in Mafft
... Quick and simple question; I am trying to align 11 very long sequences in Mafft 7.304 for Windows and always get the above error. I have tried to search to find out what it means and what I can do about it but so far haven't had much luck. Would anyone be able to tell me? I'd also appreciate a link ...
mafft written 2.3 years ago by rc1695550 • updated 2.0 years ago by Biostar ♦♦ 20
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Plotting SNP density along a chromosome from VCF files
... Hi all, I have generated VCF files from a range of samples of my study organism using a published reference genome. I now want to use these to assess where diversity is along a given chromosome; in other words I want to know the density of SNPs along chromosome 2. One way I had thought of doing t ...
genome snp written 2.4 years ago by rc1695550 • updated 2.4 years ago by sacha1.7k
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Comment: C: Difficulty with Muscle Sequence Alignment
... Many thanks for your reply; I am not sure that the problem is one of an atypical character as it seems to stop at different places each time I run it, for example another attempt produced the report "line 15: 103937 Killed". Nevertheless, would you be able to recommend a way of identifying atypical ...
written 2.4 years ago by rc1695550

Latest awards to rc16955

Popular Question 8 months ago, created a question with more than 1,000 views. For Branch Lengths in RAxML
Popular Question 8 months ago, created a question with more than 1,000 views. For Plotting SNP density along a chromosome from VCF files
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Branch Lengths in RAxML
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Plotting SNP density along a chromosome from VCF files
Popular Question 2.0 years ago, created a question with more than 1,000 views. For VCF Filtering by Multiple Parameters
Student 2.4 years ago, asked a question with at least 3 up-votes. For Plotting SNP density along a chromosome from VCF files

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