User: onestop_data
onestop_data • 160
- Reputation:
- 160
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- Trusted
- Location:
- Website:
- https://onestopdataana...
- Twitter:
- onestop_data
- Last seen:
- 6 hours ago
- Joined:
- 1 month ago
- Email:
- g****************@gmail.com
Bioinformatics scientist and blogger talking about Bioinformatics and Data analysis.
Posts by onestop_data
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... I guess it means that Metabat2 somehow was not able to bin any of your contigs. What did you use to create your BAM files prior to running it? did you make sure it was a sorted BAM?
I ran the tool today on a simulated dataset with 10 species, and it was only able to bin 2 of them. I guess in your c ...
written 3 days ago by
onestop_data • 160
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Answer:
A: Sequences alignment program
... It depends a lot on your query and database and how much memory you have available.
I wrote this blog post about [BLAST and some faster alternatives depending on some conditions.][1]
[1]: https://onestopdataanalysis.com/ncbi-blast/ ...
written 4 days ago by
onestop_data • 160
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Comment:
C: Virsorter running error
... I see. So I wonder if you named your conda environment. If you followed the tutorial on their Github page, you probably named it `virsorter `, Do you remember installing it with the following command `conda install --name virsorter -c bioconda metagene_annotator`?
If so, you need to activate the en ...
written 6 days ago by
onestop_data • 160
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... Great question. Shannon Entropy should do the job to compute complexity for a DNA string. [Here I share a script to do it.][1]. I hope it helps.
[1]: https://onestopdataanalysis.com/shannon-entropy/ ...
written 6 days ago by
onestop_data • 160
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... I agree with `Joe`. For finding phages in bacterial genome, I know `Phispy`. I have [written a step-by-step here on how to do it using FASTA to phage genomes][1].
[1]: https://onestopdataanalysis.com/finding-prophages/ ...
written 6 days ago by
onestop_data • 160
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Answer:
A: Virsorter running error
... What you get when you type `which wrapper_phage_contigs_sorter_iPlant.pl `? Maybe try `wrapper_phage_contigs_sorter_iPlant.pl --help`, conda should add the tool to the path so having `./` is probably not required. ...
written 6 days ago by
onestop_data • 160
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... I have updated the blog post. ...
written 14 days ago by
onestop_data • 160
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... Thanks. I saw the tweet, but I was not aware it was on conda already. ...
written 14 days ago by
onestop_data • 160
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... Prokka can be complicated to install because of tbl2asn dependency. I show [as part of this tutorial on how you can use it step-by-step][1] .
[1]: https://onestopdataanalysis.com/finding-prophages/ ...
written 14 days ago by
onestop_data • 160
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Answer:
A: convert gbk to fasta
... https://www.biostars.org/p/156776/ ...
written 19 days ago by
onestop_data • 160
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For A: Searching for genes in assembles genome database
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created an answer that has been accepted.
For A: Searching for genes in assembles genome database
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