I am ready to remove adapter contamination from my reads using trimmomatic. I have read the software manual and I found it include a palindrome mode to remove adapter. First, I need provide the adapter fasta file where need to specify the forward adapter and reverse adapter. I have 1 universal adapter and 24 adapters with specific index. I just do not know which is forward adapter, universal or adapters with index?
Thank you very much.
below are my adapters:
TruSeq Universal Adapter 5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT TruSeq Adapter, Index 1 5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG TruSeq Adapter, Index 2 5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG TruSeq Adapter, Index 3 5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG TruSeq Adapter, Index 4 5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG TruSeq Adapter, Index 5 5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG TruSeq Adapter, Index 6 5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG TruSeq Adapter, Index 7 5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG TruSeq Adapter, Index 8 5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCCGTCTTCTGCTTG TruSeq Adapter, Index 9 5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTG TruSeq Adapter, Index 10 5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTG TruSeq Adapter, Index 11 5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG .......