User: zhangdengwei

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zhangdengwei130
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Posts by zhangdengwei

<prev • 84 results • page 1 of 9 • next >
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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 16 days 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 23 days 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 weeks 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 6 weeks 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 6 weeks 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 6 weeks ago by zhangdengwei130
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how to get the installation history of conda
... hi all, I would like to check the history of some apps installed by `conda` on Linux, how can I get this information, like when I install or update or remove one app. Thanks very much! ...
conda written 6 weeks ago by zhangdengwei130
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Comment: C: what's the best Kmer should be set when assembling bacteria genome
... I entirely agree with you that assembly is an art. I tried several assemblers with different parameters, I would get different results. For example, I could obtain longer N50 with `unicycler` than with `spades`, but it came at a cost of shorter total assembly length. In general, it seems `spades` ou ...
written 6 weeks ago by zhangdengwei130
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what's the best Kmer should be set when assembling bacteria genome
... Hi all, I am new to bacterial genome assembly. Now I'd like to assemble a batch of single bacteria genome using Spades or IDBA-UD or Megahit. So I have no idea about which is better and how to set the best Kmer for assembly. Any suggestions would be greatly appreciated! ...
kmer genome assembly written 6 weeks ago by zhangdengwei130
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how to obtain the abundance of superclass pathway of MetaCyc when using humann2 to do function analysis
... Hi all, I have employed humann2 to do function analysis, which generated a matrix of the abundance of detailed pathways which begin with "PWY", such as "PWY-5913". And the pathway (PWY-5913) is TCA cycle VI, which is a subclass of TCA cycle. ![enter image description here][1] ![enter image descrip ...
metacyc pathway humann2 written 8 weeks ago by zhangdengwei130

Latest awards to zhangdengwei

Scholar 10 weeks ago, created an answer that has been accepted. For A: How to determine contig taxonomy from metagenome?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: How to determine contig taxonomy from metagenome?
Popular Question 10 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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