User: Gon

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

Posts by Gon

<prev • 10 results • page 1 of 1 • next >
0
votes
1
answer
322
views
1
answers
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 6 months ago by Gon10
0
votes
1
answer
322
views
1
answers
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 6 months ago by Gon10
1
vote
1
answer
322
views
1
answer
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 6 months ago by Gon10 • updated 6 months ago by Pierre Lindenbaum101k
0
votes
4
answers
933
views
4
answers
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 21 months ago by Gon10
1
vote
4
answers
933
views
4
answers
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 22 months ago by Gon10 • updated 21 months ago by guptapayal8150
0
votes
2
answers
1.1k
views
2
answers
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 2.2 years ago by Gon10
0
votes
2
answers
1.1k
views
2
answers
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 2.2 years ago by Gon10
0
votes
1
answer
1.1k
views
1
answers
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 3.1 years ago by Gon10
0
votes
1
answer
1.1k
views
1
answers
Comment: C: Analysis of resistance mutations in HIV minority variants?
... Thanks Jeremy, I know Stanford's tool but I'm afraid in doesn't work for NGS data. What I'm looking for is resistance mutations in minority variants within a patient, and I have >50,000 Illumina reads that would crash the HIVdb... But thanks anyway! ...
written 3.1 years ago by Gon10
2
votes
1
answer
1.1k
views
1
answer
Analysis of resistance mutations in HIV minority variants?
... Hi! I want to detect possible drug-resistance mutations in HIV minority variants. I'm working with a Illumina library, and I've managed to get .sam files with the reads aligned to a reference sequence, but I'm stuck on what to do next. I don't want to create a consensus of the reads, but instead, ex ...
assembly next-gen alignment written 3.1 years ago by Gon10 • updated 2.8 years ago by vandijkteghan0

Latest awards to Gon

Popular Question 3 months ago, created a question with more than 1,000 views. For Trimming an alignment in R
Popular Question 20 months ago, created a question with more than 1,000 views. For Analysis of resistance mutations in HIV minority variants?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1660 users visited in the last hour