Hi, I am working on trimming adapter using Trimmomatic, but in my trials, I have been unable to get Trimmomatic to recognize and remove the adapter sequences.

Some background:

This is 150bp, paired end Illumina data. In the result of FASTQC, the overrepresented sequences report contains no information. So I am not sure which adapter sequences files should be used. This is my adapter sequences below:

5’ Adapter:

5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’

3’Adapter：

5’-GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG-3’

In TruSeq2-PE file, my 5’adapter and 3’adapter is consistent with PCR_primer1 and PCR_primer2_rc respectively, but TruSeq2-PE file includes other sequences, such as PCR_primer1_rc、PCR_primer2.

Questions:

In this case, should I create an adapter file instead of using Truseq2-PE file directly? And if I have to create an adapter file, how should my adapter sequences be arranged? Does the index sequence should to be included in the adapter sequence?