I wanted to ask where the raw data in the HMP_2019_t2d dataset comes from. The methodology from the listed PMID (https://pubmed.ncbi.nlm.nih.gov/31142858/) indicates shotgun sequencing was only performed on nasal swabs, while the dataset in curatedMetagenomicData says data comes from stool samples. I can't find any other info regarding data origin, and I would like to download the original files to perform some additional analyses.
Thanks! However, I don't see anything regarding this study in particular. I would like to access the raw data. In the source publication cited for this dataset, only 16S sequencing is mentioned for stool samples, and I don't see any mention of whole shotgun metagenomics being applied to stool samples.
Dear @pleiramalls, @blann,
sorry for the delay! We obtained fastq files for the HMP2 study from the HMP data portal (https://portal.hmpdacc.org/). I see that site no longer exists, but the alternate site https://med.stanford.edu/ipop.html is still up. If you still have troubles accessing the raw data, let us know, as we still have raw data on file.
Sincerely,
Levi
In the inst/scripts/make-data.R it references waldronlab.io/curatedMetagenomicData/articles/articles/our-pipeline.html if that is helpful at all.
Thanks! However, I don't see anything regarding this study in particular. I would like to access the raw data. In the source publication cited for this dataset, only 16S sequencing is mentioned for stool samples, and I don't see any mention of whole shotgun metagenomics being applied to stool samples.
I wanted to ask where the raw data in the HMP_2019_t2d dataset comes from.
Thanks for your question!
Can you please post an issue at https://github.com/waldronlab/curatedMetagenomicData/issues ?
Someone from the team should be able to answer your question.
Best regards,
Marcel