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- c1_r1, c1_r2, c1_r3 from the first biological condition
- c2_r1, c2_r2, and c2_r3 from the second biological condition
Introduction
HISAT2 is is a fast transcriptome-aware mapper that is part of the new tuxedo suite of tools. These tools start with raw fastq files and produce genes, gene counts and identifies differentially expressed genes. HISAT2 uses a global, whole-genome index and tens of thousands of small local indexes to perform mapping in an extremely fast manner.