I am performing fastqc quality check on bunch of fastq files I downloaded from SRA. The fastqc report shows overall poor quality with perbase sequence content and sequence duplication level are flagged red. There is no adapter content but a lot of sequences are present in overrepresented sequences category (less than 1%). So I ran trim_galore with default parameters with paired option. The post processing looks worse then before with no improvement in sequence duplication levels or overrepresented sequences.
Now there is no adapter content which flags, so I can't run with trimmomatic with adapter sequence. Could you tell me what processing I need to do to improve sequence quality. For the particular example I posted the alignment percentage to reference genome is 88% (paired sequences). I also have some single cell sequences from the same experiments which have 60-70% alignment.