Correct Trimmomatic adapter sequence file to use?

Question

[gbatzel]

Hi,

I was told by the sequencing core that my mRNA libraries were prepared with the TruSeq Dual index adapter. They gave me two different sequences:

Index 1 (i7) Adapters GATCGGAAGAGCACACGTCTGAACTCCAGTCAC[i7]ATCTCGTATGCCGTCTTCTGCTTG

Index2 (i 5) Adapters AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT

I was wondering which Trimmomatic adapter .fasta file to use?

[reza]

if it is possible for you, use cutadapt and define your own adapters for it to remove them. Although you can create a fasta file includes your adapters for Trimmomatic