Hi all

I'm looking to export my data after assigning taxonomy to the samples in my data set.

I have used the Bio-conductor Workflow using R for bacterial 16S samples found here:

https://bioconductor.org/help/course-materials/2017/BioC2017/Day1/Workshops/Microbiome/MicrobiomeWorkflowII.html#assign_taxonomy

After assigning taxonomy with dada2, I would like to export a spread sheet with the genus/species in one column, with read counts for each of the samples.

Such as:

Bacterial Species | Sample1 | Sample 2 |

Abiotrophia spp | 248 | 150 |

Akkermansia spp | 310 | 470 |

Bacteroides spp | 265 | 340 |

etc......

I have gone through the data output files in the global environment in R-Studio and cant find any tables that have the read counts for each sample, they all seem to be the overall counts for the entire sample population

Does any one have a script?

This question has no relation to any Bioconductor package.

Excel can open any structured file, such as tab-delimited or comma-separated values. You can also specify a custom field-separator (delimiter) with Excel, which could be the pipe symbol '|'.

However, your post is lacking in descriptive information, so, nobody can help you specifically, for now.

Kevin