User: zhangdengwei

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zhangdengwei130
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Posts by zhangdengwei

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Comment: C: few genes were annotated to GO terms using online eggnog-mapper
... 1210 out of 2315 can be assigned to KEGG_ko ...
written 27 days ago by zhangdengwei130
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few genes were annotated to GO terms using online eggnog-mapper
... 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 ...
eggnog-mapper kegg go written 28 days ago by zhangdengwei130
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how to do the parametric trend analysis in R
... 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 ...
trend analysis R parametric written 12 weeks ago by zhangdengwei130
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Comment: C: error when running Mauve to re-order contigs
... no, I still have no idea. ...
written 3 months ago by zhangdengwei130
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how to select reference when constructing a SNP-based phylogenetic tree
... 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 ...
phylogenetic tree snp written 4 months ago by zhangdengwei130
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predict plasmid from bacterial WGS
... 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 ...
wgs bacteria plasmid chromosome written 4 months ago by zhangdengwei130
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how to trust the taxa profile annotated by different softwares
... 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+ ...
metaphlan3 kraken2 metagenome taxa annotation written 5 months ago by zhangdengwei130
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how to get the log file of pip in Conda
... 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! ...
conda pip written 5 months ago by zhangdengwei130
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Comment: A: how to get the installation history of conda
... I found there is a history file located at "env/conda-meta/history". Thanks! ...
written 5 months ago by zhangdengwei130
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Comment: C: how to get the installation history of conda
... It seems I cannot get the complete list using this command. ...
written 5 months ago by zhangdengwei130

Latest awards to zhangdengwei

Great Question 10 weeks ago, created a question with more than 5,000 views. For how to fix the error - Too many open files - by changing code in python3.7
Popular Question 3 months ago, created a question with more than 1,000 views. For DiffBind without replicates
Scholar 6 months ago, created an answer that has been accepted. For A: How to determine contig taxonomy from metagenome?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to determine contig taxonomy from metagenome?
Popular Question 15 months ago, created a question with more than 1,000 views. For how to fix the error - Too many open files - by changing code in python3.7

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