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User: Joseph Hughes

gravatar for Joseph Hughes
Joseph Hughes • 2.6k
Reputation:
2,570
Status:
Trusted
Location:
Scotland, UK
Website:
http://www.bioinformat...
Twitter:
blJOg
Scholar ID:
Google Scholar Page
Last seen:
4 days, 17 hours ago
Joined:
8 years, 3 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 • 227 results • page 1 of 23 • next >
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Comment: C: Method for creating an EMBL formatted annotated sequence?
... I think this should work. 1) Convert your BED to GFF using GenomeTools: [http://genometools.org/tools/gt_bed_to_gff3.html][1] 2) Using [seqret][2] from EMBOSS, convert your fasta and gff to embl follwoing this previous post: [https://www.biostars.org/p/72220/][3] Let us know how it goes. [1]: h ...
written 4 months ago by Joseph Hughes • 2.6k
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Comment: C: How to build an NJ tree with an IBS distance matrix computed by PLINK?
... What does the file look like? ...
written 4 months ago by Joseph Hughes • 2.6k
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Answer: A: Porting genome annotations from virus RefSeq to new strain: any web tools?
... [RATT][1] is a tool developed by Sanger which works well for annotation transfer from strains and closely related species. You will need an embl formatted file with the annotations and your fasta formatted sequence to start off with. Another tool worth trying but I haven't used is [GATU][2] for whi ...
written 4 months ago by Joseph Hughes • 2.6k
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Comment: C: kraken: unable to download the databases from ncbi
... I believe Derrick Wood, kraken developer, has moved on to pastures new. ...
written 4 months ago by Joseph Hughes • 2.6k
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Answer: A: kraken: unable to download the databases from ncbi
... Since NCBI updated their FTP website and decided to phase-out Genbank Identifiers (GIs), the default Kraken database update scripts do not work. My colleague @Sej Modha has written a python script that helps with updating the kraken databases: http://bioinformatics.cvr.ac.uk/blog/update-kraken-data ...
written 4 months ago by Joseph Hughes • 2.6k
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Comment: C: LoFreq outputing no SNP?
... You could try without the automatic lofreq filtering: --no-default-filter ...
written 4 months ago by Joseph Hughes • 2.6k
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Comment: C: Bacterial known pathway - the easiest way to find and download 1:1 orthologs to
... This is going to involve parsing the information from the available datasets. I suggest either parsing the "OMA groups" file in txt or xml or the "OMA Groups/Sequences in COGs format". However I could not find the important file listing the Gram positive bacteria. You may need to do this by using th ...
written 4 months ago by Joseph Hughes • 2.6k
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Comment: C: To get the name of the strains by searching assembly genome number GCF_
... you will need to do a loop in your python code to query each accession one at a time. ...
written 4 months ago by Joseph Hughes • 2.6k
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Answer: A: To get the name of the strains by searching assembly genome number GCF_
... Re-writting the following query in python should get you what you want: esearch -db assembly -query "GCF_002514765.1" | esummary | xtract -pattern DocumentSummary -element SpeciesName Sub_type Sub_value The output is: Escherichia coli strain MOD1-EC3823 ...
written 4 months ago by Joseph Hughes • 2.6k
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Comment: C: How to retrieve nucleotid sequence from gene ids of ncbis "gene" data base?
... Does your starting point have to be the taxid? The problem with starting with a taxid is that it is not very precise. It sounds like you know the two full reference genomes that you want to extract genes from so why not start from those accession numbers? ...
written 5 months ago by Joseph Hughes • 2.6k

Latest awards to Joseph Hughes

Popular Question 15 days 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 4 weeks 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 12 weeks ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Scholar 4 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Student 5 months ago, asked a question with at least 3 up-votes. For What Is The Best Search Engine To Use In Repeatmasker?
Scholar 6 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Appreciated 6 months ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Popular Question 7 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 8 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 10 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 12 months ago, created an answer that was upvoted at least 5 times. For A: Plotting Species Distribution Of Proteins
Popular Question 12 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 13 months ago, created a question with more than 1,000 views. For How To Find The Nearest Gene To A Retrotransposon Insert?
Scholar 13 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Popular Question 16 months 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
Popular Question 16 months 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
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Scholar 17 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Scholar 18 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Popular Question 19 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 19 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Popular Question 21 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 2.1 years ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Gold Standard 2.1 years ago, created a post with more than 25 bookmarks. For Reference Assembly - Mapping Reads To A Reference Genome
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