I am using Trimmomatic for adapter removal for my Truseq paired-end data (150bp). According to the Trimmomatic provided adapter file "TruSeq3-PE-2.fa" the reverse complements of index adapter sequence is used for trimming reads from R2 file and the universal adapter is used for trimming reads from R1 file.
However, it looks like that for my data the actual sequences of the index adapter is in the R1 file and the reverse complement of the universal adapter is in the R2 file. This information was also provided to me by Illumina support team. Therefore I prepared my adapter file as follows:
PrefixPE/1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG (index adapter)
PrefixPE/2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT ( reverse complement of universal adapter)
PE1_rc CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT (revcomp of PE1)
PE2_rc AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT (revcomp of PE2)
Please let me know if this adapter file I prepared is fine or is the Trimmomatic adapter file needs to be used always.