The Per sequence GC content graph gives an idea of contamination in present. How do we identify the type of contaminant? The shift in the curve towards left or right might give some idea, but how to interpret graph with multi peaks. I trimmed to remove the adopters and low quality bases but the peaks did not change.
Edit (21Aug19):: Is multiple peaks linked to samples with rRNA depletion method. I suspect this because I have both poly-A selected and rRNA depleted samples and multiple peaks occurred only in rRNA depleted samples. I further performed the downstream analysis and through Picard I observed higher intronic and intergenic bases and almost no rRNA aligned bases. Is this due to the presence of ncRNA besides mRNA?