I evaluated the quality of RNAseq data by fastqc and found that quality of sequences were not so good for following analysis. BUT, there are no over-represented sequences in quality report. As those data has been parsed by others before, I was told to remove the adapter sequences and low-quality sequences first, and then do quality evaluation. I was wondering whether adapter clipper will make fastqc report better in case that no over-represented sequences were detected by fastqc. In other words, the over-represented sequences detected by fastqc are adapters ?
Here is my fastqc command line
fastqc -o ST_read1_fastqc --contaminants TruSeq2-PE.txt -noextract ST_read1.fastq