hello everyone I am running denovo rnaseq experiment at quality control step. I can’t interpret and trim two plot duplication level and GC content at output of fastqc . I have read some articles that is not recommended to remove duplicates for differential expression analysis. I don’t know that how can I trim the outputs Here is some details of the plots.
Plot of Sequence Duplication level . Percent of seqs remaining if deduplicated 48.8% Blue line show two tower : one between 9 to 50 of X axis with maximum of Y axis= 15% and second between 50 to 500 of X axis with maximum of y axis= 8% .
Plot of per Sequence GC content Red line of this plot have two peak at points : 1- X axis= 45 and Y axis= 500000 , 2: X axis= 72 and Y axis= 720000 blue line of this plot have one peak at point : X axis= 72 and Y axis= 720000