My caution is because they have reported results for 3 primer pairs.
For your region of interest 300PE is essential even though current 600 cycle reagents gives inconsistent results. Overal Q scores for the 3' end of reads is low but a subset of reads stil have good quality. Phasing reads increases yield by enabling higher cluster density and lower Phix spike-in (at least 1.5x) and therefore increases reads with good quality 3' end.
I think Wu's method has set good benchmark if their reported lack of biase can be shown in other experiments as well. Addition of 7 base spacer would have minimal effect on the number of assembled paired reads.
For your region of interest 300PE is essential even though current 600 cycle reagents gives inconsistent results. Overal Q scores for the 3' end of reads is low but a subset of reads stil have good quality. Phasing reads increases yield by enabling higher cluster density and lower Phix spike-in (at least 1.5x) and therefore increases reads with good quality 3' end.
I think Wu's method has set good benchmark if their reported lack of biase can be shown in other experiments as well. Addition of 7 base spacer would have minimal effect on the number of assembled paired reads.
Comment