User: Joseph Hughes

gravatar for Joseph Hughes
Joseph Hughes2.7k
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

<prev • 243 results • page 1 of 25 • next >
2
votes
1
answer
121
views
1
answer
In the reformat tool of BBmap what is the meaning of Read1_linear and Read1_log
... 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 ...
reads quality bbmap written 8 days ago by Joseph Hughes2.7k • updated 7 days ago by h.mon27k
0
votes
0
answers
274
views
0
answers
Comment: C: Is there a way to calculate the maximum length at which the frequencies of k-mer
... What do you mean by information? Entropy? ...
written 4 months ago by Joseph Hughes2.7k
0
votes
0
answers
274
views
0
answers
Is there a way to calculate the maximum length at which the frequencies of k-mers can be accurately estimated?
... 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 ...
k-mer frequency written 4 months ago by Joseph Hughes2.7k
1
vote
0
answers
371
views
0
answers
Job: Deadline 26th of March: Research Database Curator
... ****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 ...
data bioinfromatics hcv job curator virus written 6 months ago by Joseph Hughes2.7k
0
votes
0
answers
979
views
0
answers
Job: Bioinformatician position at the Centre for Virus Research - Glasgow, UK
... **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 ...
phylogenetics evolution hiv outbreak job written 6 months ago by Joseph Hughes2.7k
0
votes
1
answer
300
views
1
answers
Answer: A: Phylonet -a taxa map parameter
... It doesn't like the ":" in your taxa name. ...
written 7 months ago by Joseph Hughes2.7k
1
vote
1
answer
565
views
1
answers
Comment: C: How to give merged reads as input in spades
... 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 Hughes2.7k
0
votes
2
answers
553
views
2
answers
Answer: A: Any database for downloading cancer cell-lines transcriptome differential expres
... How about expression atlas: https://www.ebi.ac.uk/gxa/home ...
written 8 months ago by Joseph Hughes2.7k
0
votes
3
answers
451
views
3
answers
Answer: A: How calculate CG content for each contig in an transcript assembly?
... 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 Hughes2.7k
2
votes
2
answers
336
views
2
answers
Answer: A: plot and show support values in consensus tree from n nj euclidean distance matr
... 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 Hughes2.7k

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
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
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
Popular Question 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
Popular Question 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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1712 users visited in the last hour