Valid Read Pairs
Read pairs with a valid R1 read and a valid R2 read are retained for further analysis.
A valid R1 read requires identified CLSs, and a UMI sequence with non-N bases.
A valid R2 read must uniquely map to the exon or intron of a bioproduct in the reference. For targeted, it must also have the correct PCR2 primer sequence at the start and an alignment match sufficient in length.