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Here are some possible benchmarking scenarios for the Unipept API
- analyse metaproteomics data sets (use sample data sets available from the Unipept website)
- analyse shotgun metagenomics data sets …
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Hi,
I am working on RNA-seq (mRNA) PE data 150x2 of microbial communities. I read a paper in which they used trinity to assemble mRNA reads. So I tried to use it for my data as well with the followin…
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Hi,
I'm having issues with **make.contigs** command.
While using **version 1.39.5**, the output of both _"stability.contigs.fasta"_ and _"stability.contigs.groups"_ were sorted at the same way, but…
ghost updated
5 years ago
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**_Hello,**_
**_I am trying to compile Mothur on a Mac machine and after running the "make" command inside the "source" directory, I get the following log (attached). But I am unable to run mothur in…
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Specifically, the call `rarefaction(sad, 'indiv')` will return an error like `Error: cannot allocate vector of size 24.7 Gb` if the sad is of a size that is often seen in microbial communities S > 20K…
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Hi there,
I am trying to run several very large microbial datasets using the MOB package (data has 370 obsv. and > 14500 variables). So far everything has run smoothly, but then I get (?a computation…
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Very good question! And one we get a lot, :). There is a difference between taxonomic OTU assigment and distance based OTU assigment. The cluster commands group sequences into OTUs based on the dis…
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Hi there,
The preprint for Distanced - https://www.biorxiv.org/content/biorxiv/early/2018/09/24/423186.full.pdf - has just been released.
Big take-home message on their benchmarking is that DADA…
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The user provided me with shared, constaxonomy and mothur created biom file. The file looked "weird" to him, more like a tree structure.
Response:
The make.biom command is designed to convert a sha…
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I ran into an unexpected mismatch and, if possible, I would like to understand what happened. I clustered my OTUs with an external software and obtained a simplified fasta (in terms of number of entri…