Hello: I have been asked to compare the quality of read one and read 2 of a illumina PE sequencing run and I am looking for the best way to represent it. I have come up with a couple of alternative:
- Count the number of bases under q 20 for each read and average it throughout the whole run, This method will lose the significance of the phred score, but it may be good to compare.
- Average the phred score for each base for each read throughout the whole run. This method may lose sensitivity since one phred quality value will represent a bunch of them.
Is there a standard way to do this? Which way is better? Thanks