Thank you for your responses, it's actually some syntax error and copy and paste errors.
I want to share that a mapping file is different from a metadata file.
I received my reads from the MRDNA facility and I preprocess the raw sequence reads with software that makes use of the mapping file. The mapping file was sent to me with the reads. When I used Keemei to validate the mapping file it differentiates the mapping file from the metadata file, in fact, I cannot edit the mapping file for the preprocessing or multiplexing of the reads, it must be in a specific format and the column number is specific and cannot be changed.
At the alpha and beta diversity stage when I need to use the metadata file, I realised the mapping file cannot be used as a metadata file, I have to format the mapping file and then validate it again with Keemei.
I do not know why this is so, but the process is complicated and may be tough for beginnings.
A mapping file is different from a metadata file, is that true?
Please advise.
This is somewhat of an edge case, based on my experience. Your mapping file here seems to specifically refer to a data format used for demultiplexing with Mr DNA based on a QIIME 1 legacy format.
The metadata file you need for alpha and beta diversity analysis may be the same as the mapping file for demultiplexing, but likely contains different information. Your metadata file describes the data you need for hypothesis testing: you main exposure, biological confounders, technical confounders, things that are neither but people assume are and therefore must be included, etc. Whether or not this overlaps with the demultiplexing information in the mapping file provided by Mr DNA is a separate issue.
Best,
Justine
PS. It’s not generally a good idea to use Dada2 on Mr DNA data because the data has already been quality filtered, which affects the ability of dada2 to accurately model it.