How I can modify the quality score to retain more reads in stacks process_radtags? I have paired-end reads from Illumina Next Seq 500.
This is my script: process_radtags -1 MAGICR1_T.fastq.gz -2 MAGICR2_T.fastq.gz -b Barcode2.txt -o /home/mdominguez/demult_MAGIC_b --renz_1 sphI --renz_2 sau3AI -E phred33 --barcode_dist_2 3 -q -r --disable_rad_check --inline_inline -i gzfastq -t 66

Best regards,

Matias