User: zhangdengwei
zhangdengwei • 130
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Posts by zhangdengwei
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... 1210 out of 2315 can be assigned to KEGG_ko ...
written 27 days ago by
zhangdengwei • 130
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... Hi all,
I was using online `eggnog-mapper (http://eggnog-mapper.embl.de)` to annotate a list of bacterial genes. But I found only 11 out of 2315 genes were successfully annotated to GO terms. All genes had hit on eggNOG ortholog. I don't why only few genes had GO term. Any explain or suggestion wou ...
written 28 days ago by
zhangdengwei • 130
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... Hi all,
I had a dataset containing three groups. Say:
A: 1, 2, 1, 3
B: 2, 4, 5, 3
C: 6, 6, 5, 7
And I would like to do the `linear trend analysis`, like the following:
![enter image description here][1]
[1]: https://i.ibb.co/4Kh6tGf/1.png
And I searched the method online and foun ...
written 12 weeks ago by
zhangdengwei • 130
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... no, I still have no idea. ...
written 3 months ago by
zhangdengwei • 130
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... Hi all,
I am new to phylogenetic tree. I have around 220 K. pneumoniae isolates. I adopted `roary` to extract their core genes, and now I wonder construct a phylogenetic tree based on SNP. Should I provide a reference for constructing the tree? If so, how should I select the reference genome? Any s ...
written 4 months ago by
zhangdengwei • 130
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... Hi all,
I have some bacterial WGS datasets, and now I'd like to separate plasmid from chromosome for each draft genome. I got to know several tools are capable of doing this (e.g. PlasmidSeeker, mlplasmids, plasmidFinder), but I am struggling to select which is best as I am new to these tools. As f ...
written 4 months ago by
zhangdengwei • 130
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hi all,
I have been troubled about the taxa annotation recently. I adopted `metaphlan3` to profile the taxa previously, about April 8, but last week I used the latest `metaphlan3` to profile the taxa again with the same command, but the taxa profile was totally different. Then I adopted `kraken2+ ...
written 5 months ago by
zhangdengwei • 130
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... Hi all,
I would like to get to know the history of `pip` in `Conda`. Because I might update an App using `pip`, but I cannot recall which version of the previous, so I'd like to check the log file of `pip` in the hope of obtaining this information. Any suggestions would be greatly appreciated! ...
written 5 months ago by
zhangdengwei • 130
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... I found there is a history file located at "env/conda-meta/history". Thanks! ...
written 5 months ago by
zhangdengwei • 130
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... It seems I cannot get the complete list using this command. ...
written 5 months ago by
zhangdengwei • 130
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