User: samuel.lipworth

Reputation:
10
Status:
New User
Location:
University of Oxford
Last seen:
an hour ago
Joined:
2 months, 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 • 12 results • page 1 of 2 • next >
0
votes
0
answers
33
views
0
answers
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 4 hours ago by samuel.lipworth10 • updated 1 hour ago by Petr Ponomarenko480
0
votes
0
answers
147
views
0
answers
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 5 weeks ago by samuel.lipworth10
0
votes
0
answers
147
views
0
answers
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 5 weeks ago by samuel.lipworth10
0
votes
0
answers
137
views
0
answers
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 7 weeks ago by samuel.lipworth10
0
votes
0
answers
135
views
0
answers
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 9 weeks ago by samuel.lipworth10
0
votes
0
answers
184
views
0
answers
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 9 weeks ago by samuel.lipworth10 • updated 7 weeks ago by Biostar ♦♦ 10
0
votes
2
answers
253
views
2
answers
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 10 weeks ago by samuel.lipworth10
0
votes
2
answers
253
views
2
answers
Comment: C: Broken vcf header, no column name?
... Thanks - I tried this but the error persists ...
written 10 weeks ago by samuel.lipworth10
2
votes
2
answers
253
views
2
answers
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 10 weeks ago by samuel.lipworth10
0
votes
1
answer
323
views
1
answers
Comment: C: Extracting N positions from fasta file
... thanks but the sequences are > 4 million bases ...
written 11 weeks ago by samuel.lipworth10

Latest awards to samuel.lipworth

Autobiographer 10 weeks ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 683 users visited in the last hour