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I spoke with one of the developers of mOTUs and he was equally surprised about this result.
If you happen to get consistently worse results we'd be interested in figuring out why.
Let us know how this goes.
Cheers,
Renato
On 1/15/20 8:53 AM, Quinten Ducarmon wrote:
> Hi Renato,
>
> Thanks for your explanation.
> I was indeed referring to the latter (If by NG-meta-profiler, in fact, you are referring to results produced with [3], then I can't say for sure). Strange that the results are so different then indeed, I will have a bit deeper look and try the pipeline with some other data.
> I will also think about whether to use, if results for some reason remain a bit worse, to use mOTUs 2.5 separately (and then to somehow also do the eggNog separately).
>
> Thanks a lot for your feedback!
> Quinten
>
> Op di 14 jan. 2020 om 15:54 schreef Renato Alves <
renato...@embl.de <mailto:
renato...@embl.de>>:
>
> Hi Quinten,
>
> If I understand your question, you are asking why the results from mOTUs 2.5 are different from, and better than, those produced with NG-meta-profiler.
>
> The reason is that NG-meta-profiler [1] uses an algorithm that is equivalent to mOTUs 1.0.
> Consequently it is expectable that results from mOTUs 2.5 are better than mOTUs 1.0 simply because the available data at the time of the construction of each of these tools was considerably different.
> Perhaps this [2] illustration will help clarify the differences.
>
> If by NG-meta-profiler, in fact, you are referring to results produced with [3], then I can't say for sure.
> The only difference between [3] and using mOTUs 2.5 directly is that the former removes reads that map to the human genome (i.e. human contamination).
> It could be that reads from some species are similar to regions in the human genome but this is an unlikely case.
> The alternative of human regions being present in some bacterial reference genomes is a known occurrence but unlikely to have a significant effect here considering how the underlying mOTUs database is constructed and used.
>
> Hope this helps,
> Renato
>
>
> [1]
https://github.com/ngless-toolkit/ng-meta-profiler/blob/master/human-gut-profiler.ngl
> [2]
https://raw.githubusercontent.com/motu-tool/mOTUs_v2/master/pics/mOTUs_versions.png
> [3]
https://github.com/ngless-toolkit/ng-meta-profiler/blob/master/extra/human-gut-profiler-motus-v2.ngl
>
>
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