sequencing 3 taxa (fungi, bacteria and archaea) together in one run on MiSeq
A beginner user of sequencing work here.
I am going to run 100 samples on Miseq to look at the soil microbial communities (for bacteria, archaea and fungi). The aim is to get about >40 000 reads per sample.
I wanted to know if I prepare library separately for bacteria, fungi and archaea and load it on the reagent kit together (multiplexing), are there any disadvantages or downsides of doing that as compared to running sequencing separately for 3 taxa?
Also, if I am loading all three prepared libraries in one run on the kit, does it mean that technically I am loading 300 samples?
I am going to run 100 samples on Miseq to look at the soil microbial communities (for bacteria, archaea and fungi). The aim is to get about >40 000 reads per sample.
I wanted to know if I prepare library separately for bacteria, fungi and archaea and load it on the reagent kit together (multiplexing), are there any disadvantages or downsides of doing that as compared to running sequencing separately for 3 taxa?
Also, if I am loading all three prepared libraries in one run on the kit, does it mean that technically I am loading 300 samples?