I have assigned 20 amplicons (~13,000 bp together) generated for 350 individuals to three 96-well plates for a variant calling analysis. So I have 3 directories with 96 x 2 fastq files (paired-end) in each directory. Summarizing 3 x 96 x 2 fastq files.
How can I identify my samples. I have done quality control analysis (FastQC) but I think I should do alignment for every individual separately.
Can you help me with describing my data set? I have never work with dataset with well plates.
Samples have been sequenced using Nextera XT.