User: rc16955

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rc1695540
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9 months, 2 weeks ago
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r******@bristol.ac.uk

Posts by rc16955

<prev • 10 results • page 1 of 1 • next >
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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 4 months ago by rc1695540
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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 8 months ago by rc1695540 • updated 4 months ago by lay_020
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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 8 months ago by rc1695540 • updated 4 months 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 9 months ago by rc1695540 • updated 9 months ago by sacha770
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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 9 months ago by rc1695540
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Difficulty with Muscle Sequence Alignment
... Hi all, I am trying to perform an alignment of 11 very long (whole chromosome) DNA sequences using Muscle 3.8.31 for Linux, but am encountering a problem. This is my input: muscle-3.8.1 -diags -in S_ratti_Chr2.fa -out S_ratti_Chr2.afa The code seems to run for a while, but then I get the fol ...
genome written 9 months ago by rc1695540
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Comment: C: VCF Filtering by Multiple Parameters
... EDIT: Just saw your edit; thanks I will take it on board :) Hi, thank you very much for your answer, it's very informative. I have now used BCFTools to filter out reads with DP>=10 and/or MQ>=30 so I have made progress, however I'm a bit stumped about how to filter according to QUAL and DP_ST ...
written 9 months ago by rc1695540
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VCF Filtering by Multiple Parameters
... Dear all, I think I need some ground-up assistance with filtering VCF files. I have generated a VCF file with samtools + bcftools after an initial alignment with bowtie2 and from what I can tell this VCF file looks as expected. Now I want to filter it in several ways and am struggling to figure out ...
snp written 9 months ago by rc1695540 • updated 9 months ago by Manuel Landesfeind1.1k
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Comment: C: Difficulty filtering VCF file with vcftools
... Hi Colin, thank you for your answer; I am now able to generate VCF files. I'm still not convinced that the line is working correctly, however. Upon examining the files I can see that the there are some SNPs present in the unfiltered file that are missing from the filtered file even though they satis ...
written 9 months ago by rc1695540
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Difficulty filtering VCF file with vcftools
... Hi all, I am trying to filter a VCF file by read depth (min 10) and mapping quality (min 30) using vcftools. I have found it quite difficult to find sample lines of anything like this, and being very new to bioinformatics and command lines in general, I'm fairly certain I'm doing something wrong. T ...
snp written 9 months ago by rc1695540 • updated 9 months ago by colindaven260

Latest awards to rc16955

Student 9 months ago, asked a question with at least 3 up-votes. For Plotting SNP density along a chromosome from VCF files

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