1. ATGC frequencies are never equal except by fluke

2. DNA sequences have periodicities or features at different size ranges

3. Sequence read in forward and reverse orientations almost always yield different biological meanings

But about how reversing alternatively, changing shuffle window size etc will change signal / noise ratio would be a multi-week study by itself

So your advice on keeping it simple and easy in terms of the coding is well taken :) Thank you!

In reply to Re^2: Reduce RAM required by onlyIDleft
in thread Reduce RAM required by onlyIDleft

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