I have the following files: assembly.fa transcripts.fa annotation.gtf
My organism is eukaryotic with introns so I was to use the hisat2 -> stringtie pipeline.
The example in the below link looks like it maps to the chromosomes/assembly and not the transcripts with HISAT2. If there were introns separating 2 exons then wouldn't the mapping be partial and the best way would be to map to the transcripts? https://davetang.org/muse/2017/10/25/getting-started-hisat-stringtie-ballgown/
Does anyone have a way to pipe hisat2 directly into stringtie? I know I'm supposed to use the --dtf flag in HISAT2 but I haven't figured out if I'm mapping to the transcripts or the assembly?