I am trying to assemble a primate transcriptome using hisat2/stringtie. First I want to index the genome using hisat2. I used both --ss and --exon to provide information on splice sites and exons.
The manual states that 8 files should be produced after indexing 1.ht2 to 8.h2t. However, I only have six files with this suffix (5.ht2 and 6.ht2 are missing) and one file is completely empty. Additionally I have 20 .rf files (0.rf to 19.rf).
Does anyone know why this is? Was there an error with indexing or can I use these files as is?