View Single Post
Old 03-16-2017, 11:30 AM   #9
thermophile
Senior Member
 
Location: CT

Join Date: Apr 2015
Posts: 237
Default

Why were you using M13? you were cloning these first?

are you giving cutadapt the degenerate primers and allowing for 2 mismatches? or giving it one of the possible non-degenerate primers and allowing for 2 mismatches? The first should work, the second should result in losing many sequences because there are degeneracies and mismatch potential which equals more than 2 differences
__________________
Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.
thermophile is offline   Reply With Quote