Hi, I have paired-end read data prepared by illumina Nextera. I'm trying to remove the adapter using Trimmomatic.
illumina adaper sequence manual (p.3) says that the following sequence is used for Read 1 and Read 2 adapter trimming. CTGTCTCTTATACACATCT
However, Trimmomatic have reverse complementary sequences as PrefixNX / 1 and PrefixNX / 2. Is it necessary to specify CTGTCTCTTATACACATCT in Trimmomatic?
NexteraPE-PE.fa (supplied by Trimmomatic):