I am looking for some input on best practices when it comes to uploading raw data from sequencing runs to repositories such as SRA, ENA or QIITA when we have multiple experiments on one chip.
It seems that these archives allow multiple runs to belong to a single project/experiment but not vice versa. I would simply split up the samples and upload separately, but they were processed together and shared some negative controls which I need to use and reference in two publications. Duplicating those controls does not seem like an ideal solution.
A method that allows the entire output of the sequencing run to be stored and identified as a single entity would also be ideal as I used the whole dataset to train my error model in DADA2.
Any experiences with this problem or advice on an archive that provides a suitable way to upload this data would be much appreciated.