User: Joseph Hughes
Joseph Hughes • 2.6k
- Reputation:
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- Location:
- Scotland, UK
- Website:
- http://www.bioinformat...
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- blJOg
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- Google Scholar Page
- Last seen:
- 3 weeks, 1 day ago
- Joined:
- 8 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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... 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 7 months ago by
Joseph Hughes • 2.6k
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... What does the file look like? ...
written 7 months ago by
Joseph Hughes • 2.6k
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... [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 7 months ago by
Joseph Hughes • 2.6k
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... I believe Derrick Wood, kraken developer, has moved on to pastures new. ...
written 7 months ago by
Joseph Hughes • 2.6k
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... 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 7 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 7 months ago by
Joseph Hughes • 2.6k
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... 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 8 months ago by
Joseph Hughes • 2.6k
0
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246
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... you will need to do a loop in your python code to query each accession one at a time. ...
written 8 months ago by
Joseph Hughes • 2.6k
0
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... 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 8 months ago by
Joseph Hughes • 2.6k
0
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... 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 8 months ago by
Joseph Hughes • 2.6k
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