I have paired-end sequencing data I would like to trim using trimmomatic. I have read 1 which matches the antisense sequence of the input and read 2 which is the sense paired-end read. I confirmed the presence of illumina adapter by fastQC. Can I simply use the provided Truseq3 (paired-end for mi-seq and Hi-seq) as adapter sequence to trim? I wonder whether I will have a problem with the antisense read?
Thanks in advance!