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When performing taxonomic profiling of MAGs, abundance information currently is not preserved. This is needed to then estimate the (relative) abundances of MAGs/taxa.
This can be done in a few steps:
map reads to MAGs.
normalize by genome length, e.g., calculate RPKM or similar. c.f., bracken uses genome length to calculate relative abundances of taxa when doing read-based profiling.
This action should probably be independent to taxonomic classification, i.e., to output a feature table of MAG abundances per sample.
mOTUs2 uses a single-copy marker-gene approach for accurately estimating taxonomic abundance from reads, but gives a good overview of the different approaches and a comparison vs. MAGs.
The text was updated successfully, but these errors were encountered:
When performing taxonomic profiling of MAGs, abundance information currently is not preserved. This is needed to then estimate the (relative) abundances of MAGs/taxa.
This can be done in a few steps:
This action should probably be independent to taxonomic classification, i.e., to output a feature table of MAG abundances per sample.
Some useful reading
The text was updated successfully, but these errors were encountered: