In Read 2, are there any negatives to incorporating reads beyond the minimum 50 bp, besides needing more computing time (i.e., taking an 'as much as possible' approach)?
In Read 2, are there any negatives to incorporating reads beyond the minimum 50 bp, besides needing more computing time (i.e., taking an 'as much as possible' approach)?
With the current aligner (STAR) and the library prep protocol used, there is an optimal range of Read 2 length to reach maximum alignment quality (between 50–150 bp). A Read 2 length of >150 bp will ultimately lead to lower alignment quality.