User: samuel.lipworth

Reputation:
20
Status:
New User
Location:
University of Oxford
Last seen:
5 months ago
Joined:
1 year, 4 months ago
Email:
s**************@medsci.ox.ac.uk

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

Posts by samuel.lipworth

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Phylogenetic tree from denovo assemblies
... Yeh but seaview cannot cope with hundreds of bacterial genomes, it crashes.. ...
written 5 months ago by samuel.lipworth20
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Phylogenetic tree from denovo assemblies
... Is there any neat way to do this? Ie to quickly get a core genome alignment from de novo assemblies and create a phylogenetic tree? I have hundreds of samples.. ...
phylogeny wgs written 5 months ago by samuel.lipworth20 • updated 5 months ago by Sergey Naumenko300
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Comment: C: ENA bulk download all fastq files in study
... thanks - sorry what I actually mean to as was how to get all of those text files for all studies for this link: http://www.ebi.ac.uk/ena/data/view/PRJNA235852 I know how to go from there using wget with the text file. ...
written 7 months ago by samuel.lipworth20
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ENA bulk download all fastq files in study
... Hi I want to bulk download all fastq files in a study from ENA http://www.ebi.ac.uk/ena/data/view/PRJEB3334 It is possible to click to the experiment and then download them but this would be very slow... any way to bulk download? ...
fastq ena written 7 months ago by samuel.lipworth20
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Answer: A: change specific bases in a fasta file
... Thanks for the help! I also managed to write my own version which seems to work to! https://github.com/samlipworth/base_changer ...
written 8 months ago by samuel.lipworth20
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Comment: C: change specific bases in a fasta file
... see below, thanks... ...
written 8 months ago by samuel.lipworth20
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Comment: A: change specific bases in a fasta file
... import csv from Bio import SeqIO from Bio.Alphabet import generic_dna from Bio.Seq import MutableSeq from sys import argv import sys script, reference, changes, out = argv changes_=open(changes, 'rb') change = csv.reader(changes_, delimiter='\t') for line in c ...
written 8 months ago by samuel.lipworth20
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change specific bases in a fasta file
... Hi, I have a list of positions I would like to change in a fasta file with the base I would like to change to tab separated as follows: 1 T 2 C 10 T 50 G etc so that eg: ATGTGTC... becomes TCGTGTC... There must be a way to do this but I can't do it - have tried to code it in biopython ...
fasta biopython written 8 months ago by samuel.lipworth20
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vcf-consensus wrong bases
... Hi I have a vcf file from which I am calling: vcf-consensus filtered.vcf.gz < NC000962.fasta > test.fasta There are bases in the new test.fasta which are different from the reference but not called as SNPs in filtered.vcf.gz - how can this be!? The VCF file is correct but I don't understand ...
vcf fasta snp written 9 months ago by samuel.lipworth20
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Answer: A: vcf at variable sites only
... Grep is the answer, sorry please close this question! ...
written 11 months ago by samuel.lipworth20

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