Moderator: jrj.healey
jrj.healey ♦ 10k
- Reputation:
- 10,500
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- Location:
- United Kingdom
- Website:
- http://www2.warwick.ac...
- Twitter:
- JRJHealey
- Last seen:
- 3 hours ago
- Joined:
- 3 years, 5 months ago
- Email:
- j*********@gmail.com
Recently finished my PhD, so now I pretend to know what I’m talking about on Bioinformatics forums...
Posts by jrj.healey
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... Please, please, don't use Excel. ...
written 3 hours ago by
jrj.healey ♦ 10k
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... Even though you've been entirely transparent about this being a homework question (which is great), and I realise this is a request for compensated help, we typically close homework posts as off topic until we've at least seen an initial attempt at the task from the poster.
We try not to do people' ...
written 16 hours ago by
jrj.healey ♦ 10k
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... What code did you use/try to match based on the similar names? ...
written 16 hours ago by
jrj.healey ♦ 10k
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... Gaps are as much a part of the alignment as the real characters - RAxML (I believe) is one of the few tools which actually incorporates the gap sites in to its tree reconstruction process. It will likely reduce your bootstrap confidence, and may lead to a harder-to-interpret tree, but that's pretty ...
written 17 hours ago by
jrj.healey ♦ 10k
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... Are you trying to run these analyses on your laptop or on the server (the short answer is you could just do both). ...
written 1 day ago by
jrj.healey ♦ 10k
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... You need a semi colon after your echo/awk command and before you call canu:
for f in *.fasta; do Gen_size=$(echo "$f" | awk -F'[_.]' '{print $3-$2}') canu -assemble -p asstest -d . genomeSize=$Gen_size -nanopore-raw $f; done
...
written 1 day ago by
jrj.healey ♦ 10k
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Comment:
C: Writing a script for quast
... Please show what your input data, desired output and any code you have already tried, looks. ...
written 1 day ago by
jrj.healey ♦ 10k
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... `conda` is like `pip`, yes, only much, much easier to use (especially if you're a noob).
It's also useful for **precisely** the reason that you don't have permission to install things, since it does everything inside your user directory. No special permissions needed. In fact, it may be one of the ...
written 1 day ago by
jrj.healey ♦ 10k
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... Well you have the right attitude, so that’s half the battle.
BioPython is a huge library, I use it regularly and still only know half a dozen of the functions anything near what I’d call ‘well’. It’s a constant learning process for us all.
It’s pretty easy to know if code is python or not, simply ...
written 2 days ago by
jrj.healey ♦ 10k
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... If you have another question, please ask another question. Answers are for answers to the main question only. ...
written 2 days ago by
jrj.healey ♦ 10k
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For A: Script/Application to create a genbank format sub-sequence
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For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
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For A: Script/Application to create a genbank format sub-sequence
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For A: Script/Application to create a genbank format sub-sequence
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