Since URA3 is on the negative strand of the plasmid read 1 of the paired end reads are actually mapped to the positive strand (unlike the rest of the genes of interest) I cannot automatically filter reads mapped to the negative strand in post-processing.
Since URA3 is on the negative strand of the plasmid read 1 of the paired end reads are actually mapped to the positive strand (unlike the rest of the genes of interest) I cannot automatically filter reads mapped to the negative strand in post-processing.