User: samuel.lipworth

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30
Status:
New User
Location:
University of Oxford
Last seen:
18 hours ago
Joined:
2 years, 3 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 16 months ago by samuel.lipworth30
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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 16 months ago by samuel.lipworth30 • updated 16 months ago by Sergey Naumenko340
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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 18 months ago by samuel.lipworth30
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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 18 months ago by samuel.lipworth30
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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 19 months ago by samuel.lipworth30
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Comment: C: change specific bases in a fasta file
... see below, thanks... ...
written 19 months ago by samuel.lipworth30
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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 19 months ago by samuel.lipworth30
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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 19 months ago by samuel.lipworth30
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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 20 months ago by samuel.lipworth30
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Answer: A: vcf at variable sites only
... Grep is the answer, sorry please close this question! ...
written 22 months ago by samuel.lipworth30

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Popular Question 16 months ago, created a question with more than 1,000 views. For ENA bulk download all fastq files in study
Popular Question 16 months ago, created a question with more than 1,000 views. For Extracting N positions from fasta file
Popular Question 16 months ago, created a question with more than 1,000 views. For change specific bases in a fasta file
Popular Question 16 months ago, created a question with more than 1,000 views. For Broken vcf header, no column name?
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