I checked my reads with fastQC and found an overrepresentation of Illumina adpaters: https://ibb.co/ftDW6sK So I trimmed it using trimmomatic and following command (75 bases Single end reads):
java -jar <path>trimmomatic-0.39.jar SE input.fastq output.fastq ILLUMINACLIP:TruSeq2-SE:2:30:10
and the same with TruSeq3 adapters:
java -jar <path>trimmomatic-0.39.jar SE input.fastq output.fastq ILLUMINACLIP:TruSeq3-SE:2:30:10
However, the output I'm getting is always the same:
Input Reads: 48046117 Surviving: 48046117 (100.00%) Dropped: 0 (0.00%) TrimmomaticSE: Completed successfully
I'm new to bioinformatics so could you please tell me if there is smth I'm missing why trimmomatic doesn't cut off any of the reads?