User: samuel.lipworth

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Location:
University of Oxford
Last seen:
19 hours ago
Joined:
1 month, 3 weeks ago
Email:
s**************@medsci.ox.ac.uk

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

Posts by samuel.lipworth

<prev • 11 results • page 1 of 2 • next >
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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 14 days 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 15 days ago by samuel.lipworth10
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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 24 days 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 5 weeks 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 6 weeks ago by samuel.lipworth10 • updated 27 days 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 7 weeks 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 7 weeks ago by samuel.lipworth10
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Broken vcf header, no column name?
... Hi, Trying to use VCF tool's vcf-compare function. I have bgzipped and tabixed indexed my files bgzip -c file.vcf > file.vcf.gz tabix -p vcf file.vcf.gz I then call vcf-compare file1.vcf.gz file2.vcf.gz but get the error: Broken VCF header, no column names? at /usr/share/per ...
vcf vcf-tools written 7 weeks ago by samuel.lipworth10
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Comment: C: Extracting N positions from fasta file
... thanks but the sequences are > 4 million bases ...
written 7 weeks ago by samuel.lipworth10
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Comment: C: Extracting N positions from fasta file
... every location at which a N is present. I have something like 36 different strains and would like to produce a list of N locations in each FASTA file and then compare these lists to find the unique N locations for each strain. ...
written 8 weeks ago by samuel.lipworth10

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