Apologies for what is an often repeated topic, but with (I believe) a new twist.
I have several RNA libraries that I amplified with the Clontech v4 Ultra-Low Input RNA kit prior to running an Nextera XT library prep. The data is back, and I am attempting to figure out how to most effectively trim adapter sequences.
I'd like to use the defaults in Trinity for the trimming of Nextera adapters as the palindromic setting will help with read-through issues more than a simple trim would. However, I am also concerned about the presence of Clontech v4 adapters (SMART primers IIa and oligonucleotide) at the ends of my sequences that need to be trimmed as well.
If I want to trim away both, do I need to just use a simple trim? Or can I do a palindromic trim with two sets of /1 and /2?
Thanks guys!
I have several RNA libraries that I amplified with the Clontech v4 Ultra-Low Input RNA kit prior to running an Nextera XT library prep. The data is back, and I am attempting to figure out how to most effectively trim adapter sequences.
I'd like to use the defaults in Trinity for the trimming of Nextera adapters as the palindromic setting will help with read-through issues more than a simple trim would. However, I am also concerned about the presence of Clontech v4 adapters (SMART primers IIa and oligonucleotide) at the ends of my sequences that need to be trimmed as well.
If I want to trim away both, do I need to just use a simple trim? Or can I do a palindromic trim with two sets of /1 and /2?
Thanks guys!