I am checking the quality control of my sequences using the Fastqc tool. For some steps, like "Per base GC content", etc., I received a warning. So, I was wondering whether I Should also take care of warning messages in the Fastqc tool or I should only care about errors! I would appreciate it if someone could help me with this, please.
Generally yes, but it depends the type of study. Remember that Fastqc was developed for bacterial genomes, mainly, so an unusually shaped distribution in that particular dataset could indicate a contaminated library. But, for example, in an amplicon 16S amplicon dataset it's expected that other modules fail (Duplicate Sequences, Overrepresented Sequences, etc.) not only GC.