Moderator: Jeroen Van Goey
Jeroen Van Goey ♦ 2.3k
- Reputation:
- 2,260
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- Trusted
- Location:
- Ghent, Belgium
- Website:
- http://jeroen.vangoey.be/
- Twitter:
- @BioGeek
- Last seen:
- 1 year, 1 month ago
- Joined:
- 10 years, 5 months ago
- Email:
- j*************@gmail.com
Just Another Genome Hacker,
Bioinformatics software developer at Applied Maths
Also known as BioGeek on the web.
Posts by Jeroen Van Goey
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7
votes
1
answer
514
views
1
answer
... On the Julia forum, there was the suggestion of creating a new "flavor" of the BioStar Handbook, but using Julia as programming language for the code examples.
https://discourse.julialang.org/t/biostar-handbook-computational-genomics-and-julia-to-be-or-not-to-be/25732
Is this allowed under the cu ...
written 13 months ago by
Jeroen Van Goey ♦ 2.3k
• updated
13 months ago by
Istvan Albert ♦♦ 84k
11
votes
2
answers
7.5k
views
9 follow
2
answers
... I have the following FASTA file, `original.fasta`:
>foo
GCTCACACATAGTTGATGCAGATGTTGAATTCACTATGAGGTGGGAGGATGTAGGGCCA
I need to change the record id from `foo` to `bar`, so I wrote the following code:
from Bio import SeqIO
original_file = r"path\to\original.fasta"
corr ...
written 4.9 years ago by
Jeroen Van Goey ♦ 2.3k
• updated
3.2 years ago by
lakshmi.bioinformatics • 20
4
votes
0
answers
1.5k
views
0
answers
... I'm using dbFetch from EBI in a project. I construct URLs from the format
https://www.ebi.ac.uk/Tools/dbfetch/emblfetch?id=[ACCESSION_NUMBER]
to retrieve sequences, e.g.:
https://www.ebi.ac.uk/Tools/dbfetch/emblfetch?id=CO069431
Accession numbers need to be of the format 1 letter + 5 numerals O ...
written 5.2 years ago by
Jeroen Van Goey ♦ 2.3k
• updated
5.1 years ago by
Biostar ♦♦ 20
0
votes
1
answer
2.1k
views
1
answers
... Input names could be changed, so I would prefer a technique that looks at the data itself. However, if that is not possible, looking at the input names might be my only/best bet.
...
written 5.8 years ago by
Jeroen Van Goey ♦ 2.3k
7
votes
1
answer
2.1k
views
1
answer
... When using the SPAdes Genome Assembler, you can use either the BayesHammer read error correction tool for Illumina reads or the IonHammer read error correction tool for IonTorrent data.
I want to use SPAdes in a general workflow and I want to know if there is an automatic way to determine if reads ...
written 5.8 years ago by
Jeroen Van Goey ♦ 2.3k
• updated
5.8 years ago by
arno.guille • 400
17
votes
3
answers
4.3k
views
8 follow
3
answers
... http://anthonyneedsajob.com/
What happened?
Anthony (Biostar user page) will soon start on an adventure in an exciting startup, but starting 1st of October 2013, he has no real source of income.
Since Anthony can not sit on his hands, he is now looking for partners to tackle exciting technical pr ...
written 6.9 years ago by
Jeroen Van Goey ♦ 2.3k
• updated
6.8 years ago by
always_learning • 1.0k
2
votes
3
answers
4.2k
views
3
answers
... r.id in the line `
records = (r for r in SeqIO.parse(input_file, "fasta") if r.id in wanted)
gives back something from the form 'gnl|TC-DB|P0A334'. So, just changing that line to
records = (r for r in SeqIO.parse(input_file, "fasta") if r.id.split('|')[2] in wanted)
will work. I will assume th ...
written 7.3 years ago by
Jeroen Van Goey ♦ 2.3k
3
votes
3
answers
19k
views
3
answers
... Are you following the Entrez Usage Guidlines? Specifically:
- For any series of more than 100 requests, do this at weekends or outside USA peak times. This is up to you to obey.
- Make no more than three requests every seconds (relaxed from at most one request every three seconds in early 2009). ...
written 7.5 years ago by
Jeroen Van Goey ♦ 2.3k
• updated
7 months ago by
RamRS ♦ 28k
0
votes
13
answers
4.7k
views
13
answers
... As far as I know there is no such button, but you can reach the moderators via the mailinglist: biostar-central@googlegroups.com
...
written 7.5 years ago by
Jeroen Van Goey ♦ 2.3k
1
vote
3
answers
9.1k
views
3
answers
... @/Vari: I have sent you an e-mail with some more information.
...
written 7.5 years ago by
Jeroen Van Goey ♦ 2.3k
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