User: samuel.lipworth

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10
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New User
Location:
University of Oxford
Last seen:
1 day, 21 hours ago
Joined:
3 months, 4 weeks ago
Email:
s**************@medsci.ox.ac.uk

Academic junior doctor in Oxford - attempting to learn bioinformatics for microbiology.

Posts by samuel.lipworth

<prev • 14 results • page 1 of 2 • next >
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list variants from concatonate snp alignment
... Hi so I have a snp alignment and I would like to use some software to classify all of my samples into a group eg 0 or 1 depending on whether they have the wild type or mutant base at any given variable site. eg sample 1 (wild type) actga Sample 2 (query) accgg so sample 2 wou ...
phylogeny python snp written 9 days ago by samuel.lipworth10 • updated 9 days ago by Pierre Lindenbaum91k
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Comment: C: Clusters of max SNP distance
... Sure: a matrix of snp distances between 4 samples eg. 0 500 0 34 4 0 19 20 3 0 So i can obviously reconstruct the phylogeny using eg ML which would show me that there is a reconstructed snp distance of <12 between samples 3 and 2, and also 4 and ...
written 5 weeks ago by samuel.lipworth10
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Clusters of max SNP distance
... Hi, I want to find all clusters of a max SNP distance of say 12 snps of 500 samples. I have a data matrix showing the SNP distances but need an algorithm to cluster them - something like hierarchical clustering with a termination at maximum distance of 12 but I'm not sure how to do this in eg R. A ...
R snp written 5 weeks ago by samuel.lipworth10 • updated 5 weeks ago by Petr Ponomarenko1.2k
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Comment: C: Analyse VCF file to find snps common to all samples in lineage
... so for example I have 22 bacterial genomes which I know from creating a snp based phylogeny tree cluster into 7 distinct lineages. I can see what these snps are on a core genome alignment multi-fasta file but this is obviously a very slow way to do it so I want to try to get this information from t ...
written 11 weeks ago by samuel.lipworth10
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Analyse VCF file to find snps common to all samples in lineage
... I have a VCF file with 22 different samples in it. Looking at the example below I know that all of the 2s come from the same lineage from looking at my phylo tree. What can I use to query the vcf so that I can group different isolates from the same lineage together and find out when there is a SNP ...
vcf snp written 11 weeks ago by samuel.lipworth10 • updated 9 days ago by Pierre Lindenbaum91k
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VelvetK long Kmers
... I have been using velvetK to estimate optimal Kmer lengths and then plugging these into velvet optimiser. When I then annotate these assemblies (using Prokka) and stick them through Roary, they seem to group by assembly length rather than true phylogeny. I know the reads are not nonsense because w ...
velvetoptimiser velvet denovo assembly written 12 weeks ago by samuel.lipworth10
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Matrix plot of deleted positions vs reference genome
... Hi, I want to plot positions which don't align to my reference genome at their respective position - eg. 1,5,7,11 for genome 1, 1,4,5,7,10,11 for genome 2. I would like the positions which don't align to be represent by bars or any other symbol so that I can compare deletions across multiple sampl ...
dna plot written 3 months ago by samuel.lipworth10
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VCF isec PERL libraries
... Hi, Trying to use vcf-isec When I call vcf-isec -n +2 file1.vcf.gz file2.vcf | bgzip -c > out.vcf.gz I get the error Unknown type [None] at /path/to/my/research/bioinformatics/vcftools_0.1.13/perl/Vcf.pm line 180. The path to Vcf.pm is definitely correct - what is going wrong? ...
vcf-tools written 3 months ago by samuel.lipworth10 • updated 3 months ago by Biostar ♦♦ 10
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Answer: A: Broken vcf header, no column name?
... Thanks I fixed it - I had to gunzip the .gz files provided to me from the pipeline and rezip them. Once I tabixed them after this it worked fine. ...
written 3 months ago by samuel.lipworth10
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Comment: C: Broken vcf header, no column name?
... Thanks - I tried this but the error persists ...
written 3 months ago by samuel.lipworth10

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