User: samuel.lipworth

Reputation:
10
Status:
New User
Location:
University of Oxford
Last seen:
2 weeks ago
Joined:
10 months ago
Email:
s**************@medsci.ox.ac.uk

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

Posts by samuel.lipworth

<prev • 24 results • page 1 of 3 • next >
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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 15 days ago by samuel.lipworth10
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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 15 days ago by samuel.lipworth10
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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 7 weeks ago by samuel.lipworth10
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Comment: C: change specific bases in a fasta file
... see below, thanks... ...
written 7 weeks ago by samuel.lipworth10
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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 7 weeks ago by samuel.lipworth10
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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 7 weeks ago by samuel.lipworth10
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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 weeks ago by samuel.lipworth10
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Answer: A: vcf at variable sites only
... Grep is the answer, sorry please close this question! ...
written 4 months ago by samuel.lipworth10
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vcf at variable sites only
... Hi, I have a vcf file which simply gives the call at every single position eg: L=C;BaseCounts=4,131,2,5;BaseCounts4=0,92,0,0;DM4=0.037;DM4L=-2.134;DP=147;DP4=47,45,0,0;DPT4L=-14.831;DZ4=0.052;DZ4L=-2.141;GC=57.430;MQ=60;MQ4=60;PCALL4=1.000;PCONS4=1.000;SBR=0 GT:DP 0/0:92 R00000039 7336 . T ...
vcf written 4 months ago by samuel.lipworth10
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(Closed) convert between vcf types
... I currently a vcf file which describes in one file the variant call for all samples at all variable positions eg: sample1, sample2, sample3, sample4, sample5 1 A A T A T 5 T T G T G I want to convert to the vcf type which shows the call for a variable positions for one sample ...
vcf written 4 months ago by samuel.lipworth10 • updated 4 months ago by Pierre Lindenbaum98k

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