combining paired-read and long-read analyses

[Stephane Plaisance]

Dear,
I have MiSeq paired-read data for one experiment and 3 PacBio HiFi runs for others (each obtained with different primer pairs in order to compare the amplicon results).
Is it possible to combine runs and obtain merged results with LotuS directly or should this be done in R by merging objects from individual runs?

Thanks for your help,

[Falk Hildebrand]

Hey,

There is no sensible way I see to combine these results.. the clustering would be influenced by combining different read technologies, lots of read filtering/clustering/post-clustering assumptions would be broken, I would except these OTUs/ASVs to make little sense. Strongly recommend to combine in R, as you suggested.

best,

Falk