User: Joseph Hughes

gravatar for Joseph Hughes
Joseph Hughes2.7k
Reputation:
2,660
Status:
Trusted
Location:
Scotland, UK
Website:
http://www.bioinformat...
Twitter:
blJOg
Scholar ID:
Google Scholar Page
Last seen:
2 days ago
Joined:
8 years, 11 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 • 238 results • page 1 of 24 • next >
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Answer: A: Phylonet -a taxa map parameter
... It doesn't like the ":" in your taxa name. ...
written 23 days ago by Joseph Hughes2.7k
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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 28 days ago by Joseph Hughes2.7k
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Answer: A: Any database for downloading cancer cell-lines transcriptome differential expres
... How about expression atlas: https://www.ebi.ac.uk/gxa/home ...
written 4 weeks ago by Joseph Hughes2.7k
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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 4 weeks ago by Joseph Hughes2.7k
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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 4 weeks ago by Joseph Hughes2.7k
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Answer: A: How to give merged reads as input in spades
... It is unclear whether you have reads that are interlaced or joined. If you have joined the reads together because they overlap, then these new merged reads can be specfied as a single-end reads along with the other paired-end reads: spades.py -1 read1.fq -2 read2.fq -s merged.fq -o spades_test ...
written 4 weeks ago by Joseph Hughes2.7k
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Comment: C: How to submit a Pilon fasta output to the RAST annotation service using Shell or
... Are you talking about MG-RAST? ...
written 4 weeks ago by Joseph Hughes2.7k
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Comment: C: Assembling ESTs and illumina reads
... I'm not having much luck running iAssembler. At the moment, I'm thinking of doing a de-novo transcriptome assembly with Trinity and then using CPA3 to merge my ESTs with the trinity-assembled transcripts. ...
written 4 weeks ago by Joseph Hughes2.7k
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Assembling ESTs and illumina reads
... I am trying to improve the annotations in a region of the Sheep genome and have compiled at set of 60 Sanger sequenced ESTs from sheep which I would like to assemble with a set of 2,863,891 sheep Illumina reads from a transcriptomic study. These are the reads that mapped to a syntenic region in the ...
ests illumina de-novo transcriptome written 4 weeks ago by Joseph Hughes2.7k
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Answer: A: Is there a tool for making a synteny blocks of a gene with its downstream and up
... Perhaps, something like [genoplotR][1] would do the trick. I found it useful for looking at synteny of genes in large virus genomes. [1]: http://genoplotr.r-forge.r-project.org/ ...
written 12 weeks ago by Joseph Hughes2.7k

Latest awards to Joseph Hughes

Scholar 4 weeks ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Scholar 4 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Appreciated 11 months ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Scholar 13 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Student 13 months ago, asked a question with at least 3 up-votes. For What Is The Best Search Engine To Use In Repeatmasker?
Appreciated 15 months ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Scholar 15 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Popular Question 15 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 16 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 19 months 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 20 months ago, created an answer that was upvoted at least 5 times. For A: Plotting Species Distribution Of Proteins
Popular Question 20 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 21 months ago, created a question with more than 1,000 views. For How To Find The Nearest Gene To A Retrotransposon Insert?
Scholar 22 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Scholar 2.1 years ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Scholar 2.2 years ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Which simulator to use for generating fastq reads from a population of haploids

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