Based on FastQC result, I have two overrepresented sequence. One is my TruSeq Adapter sequence and another seems like a contaminated sequence (below) AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTT
I would like to remove/trim this contaminated sequence from my fastq file before mapping, but I don't know how to do it. I heard that this can be done with fastq-grep but not sure how to use grep tool to remove the contaminated sequence.
Thank you for your help in advance.