How is it connected to FastQC?

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FastQC is a process of Quality Control evaluation of the RNAseq reads. You can run FastQ data through FastQC to determine how good the reads are. Often, there are some reads that are not full length and thus the QC score goes down below acceptable levels towards the end of the read length (about 65-72 bases). After trimmomatic, the QC output should indicate only high quality reads remain in your data.