Hello,
I have a quick question, I have processed 4 libraries using the exact same code and dada2 perimeters as suggested in a previous post. For the most part, I have gotten great merging values for 3 libraries, but for one of the libraries, I just cannot manage to get anything good. The table.qza file used to select the dada2 perimeter looks great, or so I think, as it is comparable to the other 3 libraries but yet, dada2 is not giving me great results.
I have also noticed that even though all libraries have a comparable number of samples (+- 96) they all took about 1.35 min to process through DADA2, but when I process the 3rd library, with the exact same parameters, it takes about 5 hrs and 45 minutes to process. I feel like something is off and I have compared the imported files and demuxed files and they seem fine so I am not sure why I am having such a hard time with the DADA2 step for this library.
I am not sure how to proceed. I have tested various parameter on this library, including the parameters I used for the other libraries and everything just takes forever to process and results in low values. Can you please help me in understanding what I could be doing wrong or what I am missing?
I have attached both the table and stats outputs from DADA2 and the trimmed demux file used to select DADA2 parameters.
Fungal-demux-trimmed-3.qzv (304.3 KB)
Fungal-2-Stats-dada2-209-201.qzv (1.2 MB)
Fungal-2-Table-dada2-209-201.qzv (731.7 KB)