I have just received the output from a Hi Seq run targeting the V4 region and using v2 sequencing chemistry (2 x 300bp).
It seems as though there are much more raw reads than when I have used Mi Seq runs.
In addition, when I checked the files with FastQC, the F reads are excellent, and the R reads pass the QC (>30) although there is some drop off after 250bp, so I will trim to 250bp before proceeding with the analysis.
I am trying this workaround in order to alleviate the difficulties associated with the v3 Mi Seq chemistry.
Should the higher numbers of raw reads be expected, given that this is a Hi Seq run?
Can I use the Mothur Mi Seq protocol as usual with this Hi Seq data?
Thank you in advance