Hi Everyone, I have done RNA-seq (75 bp paired-end; 50 million reads per sample) on some samples to assess differential expression. Initial FastQC report showed some sequence duplications issue. Despite that, I did the alignment and imported the resulting BAM files in Seqmonk for further analysis. RNASeq QC report in SeqMonk indicated rRNA contamination. So, I went back and removed the rRNA reads using sortmerna. In some cases, the rRNA read files are huge. However, when I do a FastQC analysis on the files without rRNA reads, I do not see a change in number of reads or sequence duplication levels compared to original raw files. I don't know how is it possible. Suggestions and solution please. Thanks.