User: agata88
agata88 • 800
- Reputation:
- 800
- Status:
- Trusted
- Location:
- Poland
- Website:
- http://bioidea.com.pl/en
- Last seen:
- 3 months, 3 weeks ago
- Joined:
- 4 years, 11 months ago
- Email:
- a***************@o2.pl
Posts by agata88
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... Hi all!
I would like to download FASTA protein sequences from all Escherichia coli strains. At the Ensembl Bacteria page I see that I should download 2 681 files (https://bacteria.ensembl.org/info/website/ftp/index.html).
I would like to do it in programmatically way and use Ensembl Rest API. Unf ...
written 4 months ago by
agata88 • 800
• updated
4 months ago by
Ben_Ensembl • 1.5k
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... Thanks! I will try that tools. Best, Agata ...
written 5 months ago by
agata88 • 800
1
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1
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... Hi all!
Do you recommend any tool that can predict surface proteins in selected bacteria strain e.g. Escherichia coli?
Many thanks for any suggestions,
Best,
Agata ...
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... I know how to do it in multiple steps, I am wondering if there is a ready-to-go tool. Best, Agata ...
written 8 months ago by
agata88 • 800
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... Well, I am not asking about simple SNP identification but about whole multiple genome comparison for marker identification. Sorry if I didn't make it clear. Best, Agata ...
written 8 months ago by
agata88 • 800
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... Hi all!
Do you know any tool that can compare multiple genomes and define differences between them (genetic variants) and cluster them according to close identity?
Many thanks to any help,
Best,
Agata ...
written 8 months ago by
agata88 • 800
0
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Comment:
C: Qiime2 - make table.gza
... Hi, I was, but somehow I missed it. Thanks a lot! Best, Agata ...
written 10 months ago by
agata88 • 800
0
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... Hi all!
I am new with Qiime2 and any kind of help would be much appreciated.
I have abundance results for every taxonomy (phylum - genus) in Excell format. I would like to perform alpha and beta diversity with Qiime2. How can I convert data into table.gza file?
Many thanks to any suggestions.
...
written 10 months ago by
agata88 • 800
0
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1
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... I am also running R version 3.6.0 and Gviz 1.28.0, so I don't know why this is not working for me...
For second question, thank you for tips! I will dig a little more. Best, Agata ...
written 11 months ago by
agata88 • 800
0
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1
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577
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1
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... Hi all!
I am having trouble with Gvis library and plotTracks function. Here is my code:
ideogram <- IdeogramTrack(chromosome = "chr4",genome="hg38")
axis <- GenomeAxisTrack()
plotTracks(list(ideogram, axis),from=189233986,to=189234447)
Unfortunately, it is not plotting anything. ...
written 11 months ago by
agata88 • 800
• updated
11 months ago by
benformatics • 1.6k
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