I am wondering on how I should trim my reads for a metagenomics study. Surely, I don't need extra stringent conditions as Q=30. But how low can I get to keep my reads numerous and long? I have considered checking average quality first and then trimming, say, at half the average quality. But then I'd have different trimming settings for different runs.
What are your ideas on balancing sensitivity/specificity in this case?
That makes sense I guess, I'll just set Q=4 to make sure nts are more likely to be right than wrong. I guess there's no way of finding out if it works other than testing it
Mapper/Aligner and VariantCaller have there own logic how to handle bad quality values. Just let them do their job.
In most cases you will have bad quality values at the end of your reads. If the Mapper/Aligner isn't satisfied with it, it will clipp those bases by it's own.