Hello I struggled with alignment step in rna-seq pipeline (my data is whole transcriptome of prokaryote by using direct RNA sequencing method with nanopore). The manuals and tutorials of alignment to reference transcriptome that I found were short read only. I have tried using minimap2 for alignment the RNA from nanopore FASTQ file to reference genome (FASTA) and gene annotation file (GTF) (this tools need convert the GTF,GFF3 to BED first). However, the SAM result I got is exactly the same to alignment to reference genome (FASTA file only). So my question is what is difference of output that they generate in SAM file between mapping with mapping to reference genome (FASTA) only and mapping with reference genome (FASTA) with gene annotation file (GTF or GFF). Thanks in advance!