User: Gon

gravatar for Gon
Gon10
Reputation:
10
Status:
New User
Location:
Edinburgh, UK
Last seen:
1 month, 1 week ago
Joined:
4 years, 9 months ago
Email:
y***********@gmail.com

Posts by Gon

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Trimming an alignment in R
... Hi jbt38! Following my example, I would export the sliced alignment into a new file like this: write.dna(gene_wanted, file="gene_wanted.fas", format="fasta", nbcol=-1, colsep="") Hope it's useful. ...
written 6 weeks ago by Gon10
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Sequence clustering based on provided genetic distances
... Hey there! I was wondering if anybody knows any method that allows you to cluster sequences according to pairwise genetic distances. Ideally, I would be able to provide a genetic distance matrix and the method would group them, based on a cutoff also provided or optimised by the method according t ...
sequence alignment genetic distance clustering written 10 weeks ago by Gon10
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Comment: C: Extracting specific metadata from SRA runs
... Thanks Pierre, this is actually helpful: I still have to wait for all sample.xml files to unzip but at least in this format the data is much easier to work with and I will be able to parse data from it. ...
written 2.2 years ago by Gon10
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Comment: C: Extracting specific metadata from SRA runs
... For example, for the accession name ERS446847 I want to parse the information corresponding to the sample attributes with tags "geographic location (country and/or sea)" and "collection date", which from visual inspection of the file `ERA305021.sample.xml` (ERA305021 is the submission code for that ...
written 2.2 years ago by Gon10
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Extracting specific metadata from SRA runs
... Dear everyone, I want to retrieve reads from NCBI that correspond to *Staphylococcus aureus* isolated from specific hosts (eg. Bovine, swine). I also want to extract metadata (such as collection place and/or date) from those isolates. Searching “Staphylococcus aureus” on SRA (https://www.ncbi.nlm.n ...
ncbi sra sradb genomics metadata written 2.2 years ago by Gon10 • updated 7 months ago by Rob0
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Answer: A: How to get the outgroup of a rooted tree in R
... Thanks! Ideally I would've liked to find a function or a more automatized method, but sometimes that's asking too much. I will use your recommendation, thanks a lot. ...
written 3.5 years ago by Gon10
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How to get the outgroup of a rooted tree in R
... Dear all, I need to identify the outgroup sequence(s) in a series of phylogenetic rooted trees. I've been trying to look for any function in ape or phangorn that does this, but so far I haven't found one. Any ideas? Thanks! Gon ...
R phylogenetics ape phangorn written 3.5 years ago by Gon10 • updated 3.5 years ago by guptapayal8150
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Answer: A: Trimming an alignment in R
... Thanks Andrew! Eventually I managed to do it with ape, converting the object type DNAbin in a matrix, that way you can subset the usual way with square brackets. If you initially import the alignment from a fasta file using the argument "as.matrix=TRUE" you can skip the step of converting the DNAbin ...
written 3.8 years ago by Gon10
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Trimming an alignment in R
... Hi! I was wondering if anyone could help. I'm using the package ape in R and I want to trim an alignment of class DNAbin, this is, selecting portions of the alignment between two nucleotide positions. For example, I want all the sequences of my alignment but only between the nt positions 1503 and 30 ...
R alignment ape written 3.8 years ago by Gon10 • updated 20 months ago by Biostar ♦♦ 20
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Comment: C: Analysis of resistance mutations in HIV minority variants?
... Oh, that's quite different, then! In that case, it's worth trying (I already applied for a user key). I didn't understand you the first time, sorry. Thanks for the info! ...
written 4.8 years ago by Gon10

Latest awards to Gon

Popular Question 19 months ago, created a question with more than 1,000 views. For Analysis of resistance mutations in HIV minority variants?
Popular Question 19 months ago, created a question with more than 1,000 views. For Trimming an alignment in R
Popular Question 23 months ago, created a question with more than 1,000 views. For Trimming an alignment in R
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Analysis of resistance mutations in HIV minority variants?

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