Hi,

Currently i am performing QC on new RNA-seq data. My fastq files were generated by Paired-end sequencing with a read length of 151 bases. Total rna was extracted and depleted of rRNA. RNA was isolated from a viral infection experiment. Upon looking at the fastqc output of the un-trimmed fastq files, most of the parameters were satisfied except for those mentioned above. I did get a warning for over represented sequences but these were found to be sequences related to the virus genome due to cellular replication.

My question is, that is this issue due to adapters of more likely a subsequence of the experiement conditions. I have attached pictures of output for failed modules.

Thanks.