User: Joseph Hughes
Joseph Hughes • 2.7k
- Reputation:
- 2,690
- Status:
- Trusted
- Location:
- Scotland, UK
- Website:
- http://www.bioinformat...
- Twitter:
- blJOg
- Scholar ID:
- Google Scholar Page
- Last seen:
- 11 hours ago
- Joined:
- 9 years, 6 months ago
- Email:
- h************@gmail.com
My interests are in the evolution of host-parasite interactions. Phylogenetics and bioinformatics form an important aspect of my research. You can see my most recent publications http://www.mendeley.com/profiles/joseph-hughes/ http://twitter.com/blJOg
Posts by Joseph Hughes
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... This is an example output from bbmap's reformat.sh tool using the following command:
reformat.sh in1=input_R1.fq in2=input_R2.fq qhist=quality.txt
I've looked on the [website][1] and search biostars and seqanswers to try to understand what the column labels mean, with no luck.
#BaseNum R ...
written 8 days ago by
Joseph Hughes • 2.7k
• updated
7 days ago by
h.mon ♦ 27k
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274
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... What do you mean by information? Entropy? ...
written 4 months ago by
Joseph Hughes • 2.7k
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... A reviewer has asks us to calculate the theoretical range of optimal k-mer sizes for a given database of viral sequences, stating:
"The optimal range lies between: the minimum size for which a maximum number of different features can be found in the string (the viral genome); and the maximum length ...
written 4 months ago by
Joseph Hughes • 2.7k
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... ****Research Database Curator**
**Vacancy Ref: 024569**
**Grade 6: £28,660 - £32,236 per annum, pro rata for 20 hours per week**
**This post is part time (20 hours per week) and has funding until 31 March 2020.****
The MRC-University of Glasgow Centre for Virus Research (CVR) (http://www.cvr ...
written 6 months ago by
Joseph Hughes • 2.7k
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... **Bioinformatician**
**Closing date for application: 14th of March**
Reference Number 024544 Location Garscube Campus College / Service COLLEGE OF MVLS Department RI INFECTION IMMUNITY & INFLAMMATION Job Family Research And Teaching Position Type Full Time Salary Range £28,660 - £32,236
Job Pu ...
written 6 months ago by
Joseph Hughes • 2.7k
0
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300
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... It doesn't like the ":" in your taxa name. ...
written 7 months ago by
Joseph Hughes • 2.7k
1
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565
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... The format of the sequences and the identifiers in out_ecoli and out_salmonella should enable you to determine that. ...
written 7 months ago by
Joseph Hughes • 2.7k
0
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2
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553
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2
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... How about expression atlas: https://www.ebi.ac.uk/gxa/home ...
written 8 months ago by
Joseph Hughes • 2.7k
0
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3
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451
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... You could use [compseq][1] from EMBOSS, you can get the observed and expected of each dinucleotide. Or if you are looking for CpG islands, use [newcpgreport][2]. EMBOSS accepts fasta as an input format.
[1]: http://emboss.sourceforge.net/apps/cvs/emboss/apps/compseq.html
[2]: http://emboss.sour ...
written 8 months ago by
Joseph Hughes • 2.7k
2
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336
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2
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... Using the [boot.phylo][1] function in the ape package in R, you can do the following:
data(woodmouse)
fun <- function(x) as.phylo(hclust(dist.dna(x), "average"))
tree <- fun(woodmouse)
bstrees <- boot.phylo(tree, woodmouse, fun, trees = TRUE)$trees
boot <- prop.clade ...
written 8 months ago by
Joseph Hughes • 2.7k
Latest awards to Joseph Hughes
Great Question
3 months ago,
created a question with more than 5,000 views.
For Reference Assembly - Mapping Reads To A Reference Genome
Great Question
3 months ago,
created a question with more than 5,000 views.
For Reference Assembly - Mapping Reads To A Reference Genome
Appreciated
3 months ago,
created a post with more than 5 votes.
For A: Plotting Species Distribution Of Proteins
Popular Question
4 months ago,
created a question with more than 1,000 views.
For How to check the type of identifier from ensembl?
Popular Question
6 months ago,
created a question with more than 1,000 views.
For How to check the type of identifier from ensembl?
Scholar
8 months ago,
created an answer that has been accepted.
For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Scholar
11 months ago,
created an answer that has been accepted.
For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Popular Question
14 months ago,
created a question with more than 1,000 views.
For DEADLINE 18th of March: 2nd Annual Training Course on Viral Bioinformatics and Genomics
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Plotting Species Distribution Of Proteins
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15 months ago,
created a question with more than 1,000 views.
For DEADLINE 18th of March: 2nd Annual Training Course on Viral Bioinformatics and Genomics
Popular Question
16 months ago,
created a question with more than 1,000 views.
For DEADLINE 18th of March: 2nd Annual Training Course on Viral Bioinformatics and Genomics
Appreciated
18 months ago,
created a post with more than 5 votes.
For A: Plotting Species Distribution Of Proteins
Scholar
20 months ago,
created an answer that has been accepted.
For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Student
20 months ago,
asked a question with at least 3 up-votes.
For What Is The Best Search Engine To Use In Repeatmasker?
Appreciated
22 months ago,
created a post with more than 5 votes.
For A: Plotting Species Distribution Of Proteins
Scholar
22 months ago,
created an answer that has been accepted.
For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Popular Question
22 months ago,
created a question with more than 1,000 views.
For Using Ensembl API to get a Gene ID from a protein ID
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23 months ago,
created a question with more than 1,000 views.
For Using Ensembl API to get a Gene ID from a protein ID
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For Using Ensembl API to get a Gene ID from a protein ID
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2.3 years ago,
created a question with more than 1,000 views.
For Using Ensembl API to get a Gene ID from a protein ID
Good Answer
2.3 years ago,
created an answer that was upvoted at least 5 times.
For A: Plotting Species Distribution Of Proteins
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For How To Find The Nearest Gene To A Retrotransposon Insert?
Scholar
2.4 years ago,
created an answer that has been accepted.
For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Teacher
2.6 years ago,
created an answer with at least 3 up-votes.
For A: Plotting Species Distribution Of Proteins
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For Two Bioinformatician Job Openings At The Mrc - University Of Glasgow Centre For Virus Research
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