I have some RNA seq data. I did fastqc and multi QC on the data and I have some questions about the output and how to proceed. I was checking the quality scores for the bases and the mean for my samples is higher than 35 which seems to be good. However, when I look at the individual fastqc files I noticed that even though the per base sequence quality seems to pass the check the error bars are really big. For example the mean could be 38 but the error bar will reach 24. Should I be concerned about that?
Also, I am getting two peaks on the per sequence GC content. I was reading about it and it seems that this could indicate some kind of contamination. I am planning to use STAR to align the data and then check the GC content on the mapped and unmapped reads. I am also planning to blast some of the overrepresented sequences. Is there anything else I can do to identify the source of contamination and check if it interferes with the mapping?