Can I use the singleM output based on the individual genes for analysis?

[lcamVz]

I have the output of singleM. But I wanted to ask if I can use the genes for example calculate and visualize the individual genes richness, etc or this is meant to use the singleM as a whole without any subset?

[wwood]

Hi,

There is nothing wrong with using individual genes to answer questions about diversity. Be watchful of sequencing error though, since they OTUs are 100% clustered and there is no error correction like e.g. dada2 applied.

[lcamVz]

Hi

Thank you so much for the clarification greatly appreciated.

I am curiuous now could the sequences extracted of the singleM by modification of the intermidiate files be used to be ran in dada2 or similar, like pipelines such as PIPITS which extracts the ITS region before the OTU clustering or that would be too much to implement?

[wwood]

Hi,

Error correction on the OTU level similar to amplicons is something that might be possible. We have never really looked into it. We instead rely on the implicit error correciton that happens as part of converting the OTU table into a taxonomic profile, where multiple genes can be used to correct each other. Would be interested in results if you were to try it. One thing to beware of - the number of sequences in a SingleM OTU is usually much lower than the number in an amplicon dataset.