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 10 fastq files for the PVL group (samples from JVB-R1 to JVB-R10), the 5 fastq files for the control group (samples from JVB-R11 to JVB-R15), and the fasta file with the GRCh38.95 reference genome and the associated GTF file.
