User: vincentpailler

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Posts by vincentpailler

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Comment: C: CheckM and strain heterogeneity
... I retried to use CheckM on another dataset, I get this result : ![checkM][1] I don't know what I have to think about my result. I do not have any contamination or any heterogeneity.. Does that mean that the bin correspond to related species ? And how do you calculate the completness of the differe ...
written 3 months ago by vincentpailler100
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Comment: C: CheckM and strain heterogeneity
... Thanks for the answer. They have a low completness because they have a very low contamination, right? For the moment, there is not a real proof of taxonomic unit ? And if yes, at what level? ...
written 3 months ago by vincentpailler100
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Comment: C: CheckM and strain heterogeneity
... Also, can we consider each bin here as a MAG? If yes, how do you consider a "good" MAG, or at least a bin which really corresponds to a real MAG? I read a paper that says a "real" MAG is a one with <10% contamination or completness is 5*contamination>50 . It looks right for you? ...
written 3 months ago by vincentpailler100
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Comment: C: CheckM and strain heterogeneity
... ![CheckM results][1] Thanks for your answer. It is more clear for me. If you look at my CheckM results, they look pretty bad or nonetheless, I can say that the bins found are unrelated and do not correspond to a same species, right? [1]: https://i.postimg.cc/hvPSHXCK/CheckM.png ...
written 3 months ago by vincentpailler100
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CheckM and strain heterogeneity
... Hello, I don't understand something with the CheckM software. I read the documentation about the "strain heterogeneity" and it is said that the heterogeneity is determined from the number of multi-copy marker pairs which exceed a specified amino acid identity threshold (default = 90%) . But I don' ...
checkm written 3 months ago by vincentpailler100 • updated 3 months ago by Mensur Dlakic2.1k
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Comment: C: Problem to run checkm.
... Ok I got it. And is there is a file where the output is stored? I can't find it. ...
written 4 months ago by vincentpailler100
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Comment: C: Problem to run checkm.
... You meant "0% contamination" no? ...
written 4 months ago by vincentpailler100
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Comment: C: Problem to run checkm.
... I only shew you the head of the output. I got some other lineages : UniRef90_65 p__Proteobacteria (UID3880) 1495 261 164 188 60 13 0 0 0 27.85 5.12 38.46 UniRef90_71 p__Euryarchaeota (UID3 ...
written 4 months ago by vincentpailler100
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Comment: C: Problem to run checkm.
... I only need to add the `-g` option to work on proteic sequences. ...
written 4 months ago by vincentpailler100
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Comment: C: Problem to run checkm.
... The `-g` option worked. Thanks. -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Bin Id Marker lineage # genomes # markers # mark ...
written 4 months ago by vincentpailler100

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