User: Joseph Hughes

gravatar for Joseph Hughes
Joseph Hughes2.3k
Reputation:
2,300
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Location:
Scotland, UK
Website:
http://www.bioinformat...
Twitter:
blJOg
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Last seen:
4 hours ago
Joined:
7 years, 8 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 • 207 results • page 1 of 21 • next >
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How to download an unspliced transcript for a given Ensembl ID using the perl API
... This is the code snippet I have so far: my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' ); # Get the 'ensemblID' gene from human my $gene = $gene_adaptor->fetch_by_gene_stable_id( 'ENSG00000099889'); print "GENE ", $gene->stable_id(), "\n"; print_DB ...
ensembl unspliced transcript written 4 hours ago by Joseph Hughes2.3k
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Answer: A: Extract reads from fasta file (specific read_names)and make a new fasta file
... First make sure your fasta sequences in sample1.fa are on a singleline rather than warpped around multple lines: awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }' sample1.fa > sample1_singleline.fa Then simply `grep` the identifier/name of t ...
written 11 hours ago by Joseph Hughes2.3k
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Answer: A: Perl code for counting number of bases
... `chomp` removes the end of line character `split //` splits the string into characters that are added to the hash with `$bases{$_}++` whilst incrementing with `++`. The `for` is for looping through the array which is produced by `split //` Then if you reach the end of the file `eof` you sort the ...
written 7 days ago by Joseph Hughes2.3k
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Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
... A wide range of formats exist for representing the comparisons of different sequences to each other: blast tabular, blast xml, psl, pslx, SAM/BAM, BED Most of these formats can be converted from one format to another. Sometimes the format is lossless allowing for the original data to be perfectly ...
psl bed tutorial sam blast written 8 days ago by Joseph Hughes2.3k
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Answer: A: How To Extract Title And /Isolation_Source From A List Of Genbank Accession Numb
... You might be able to do that using [genbankr][1] from Bioonductor. And another one that looks good is [biofiles][2]. [1]: https://bioconductor.org/packages/release/bioc/html/genbankr.html [2]: https://github.com/gschofl/biofiles ...
written 8 days ago by Joseph Hughes2.3k
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Answer: A: Where to find Drosophila melanogaster de novo transcript assembly data?
... In this paper, you can find a list of SRA accessions for Drosophila short reads. They have also provided the statisitcs for different de-novo assemblers: [Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study][1]. Unfortunately, they do not seem to provide the a ...
written 8 days ago by Joseph Hughes2.3k
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Answer: A: Zoomable phylogenetic tree as interface to mySQL database
... The list of options is endless. I think your question might benefit from being a bit more specific. Does this have to work in a web-browser? Does it have to be in a particular programming language? Do the nodes need to have lables? Here are a few options: [http://iphylo.blogspot.co.uk/2007/08/visu ...
written 20 days ago by Joseph Hughes2.3k
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Job: Research Database Engineer, MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
... Research Database Engineer Vacancy Ref: 018930 Salary: Grade 6, £28,098 – £31,604 per annum We are seeking to appoint a research database engineer to join our expanding bioinformatics team at the MRC-University of Glasgow Centre for Virus Research (CVR) (http://www.cvr.ac.uk/). You will be involv ...
database engineer job virus written 20 days ago by Joseph Hughes2.3k • updated 20 days ago by genomax37k
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Answer: A: findMotifsGenome.pl Homer using "RNA"
... I think you need to use -rna, it looks like you are forgetting the hyphen. From the website: Search for RNA motifs ("-rna") If looking at RNA data (i.e. Clip-Seq or similar), this option will restrict HOMER to only search the + strand (relative to the peak), and will output RNA motif logos (i.e. ...
written 10 weeks ago by Joseph Hughes2.3k
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Answer: A: To retrieve bacterial Phylum and Class information from a set of tax id
... You could use NCBI eutilities with esarch and efetch. From the xml output you can extract the full lineage: esearch -db taxonomy -query "txid11053 [Organism]" | efetch -format xml | xtract -element Lineage ...
written 10 weeks ago by Joseph Hughes2.3k

Latest awards to Joseph Hughes

Scholar 11 hours ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Appreciated 11 hours ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Popular Question 8 days 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 7 weeks 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 3 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 5 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 5 months ago, created an answer that was upvoted at least 5 times. For A: Plotting Species Distribution Of Proteins
Popular Question 6 months ago, created a question with more than 1,000 views. For How To Find The Nearest Gene To A Retrotransposon Insert?
Scholar 6 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Scholar 10 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 12 months ago, created a question with more than 1,000 views. For Which simulator to use for generating fastq reads from a population of haploids
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Popular Question 14 months ago, created a question with more than 1,000 views. For Which simulator to use for generating fastq reads from a population of haploids
Appreciated 18 months ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Great Question 19 months ago, created a question with more than 5,000 views. For Help With Understanding The Output Of Codeml From The Paml Package
Gold Standard 19 months ago, created a post with more than 25 bookmarks. For Reference Assembly - Mapping Reads To A Reference Genome
Popular Question 19 months ago, created a question with more than 1,000 views. For Why Shouldn'T I Use Masking When Doing A Reference Alignment?
Student 19 months ago, asked a question with at least 3 up-votes. For How To Find The Nearest Gene To A Retrotransposon Insert?
Popular Question 24 months ago, created a question with more than 1,000 views. For Reference Assembly - Mapping Reads To A Reference Genome
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Reference Assembly - Mapping Reads To A Reference Genome

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