Hi, I am new to reference-based RNA-Seq analysis on Galaxy.
I did FASTQC followed by MultiQC on my read files before and after trimming with trimmomatic. I want to know if there’s any use of doing the Quality Control, other than seeing the adaptor content decrease after trimming.
Do we at any point take decisions like, rejecting the reads on finding poor quality sequences (for e.g. when the boxes enter the pink zone of ‘per base sequence quality’ in FASTQC reports)?
Also is there any us of the MultiQC report other than the Adaptor Content section?