2.1. - TOPHAT/HISAT2 & CUFFLINKS
“Tophat/Hisat2 & Cufflinks” is recommended for RNA-seq studies when the reference genome has an annotation GTF/GFF file. To complete the tutorial for this protocol, you will need the four fastq files for the infected group (samples from BI1 to BI5), the four fastq files for the control group (samples from BC1 to BC4), and the fasta file with the fSpaAur1.1 reference genome and the associated GTF file.
