I have a fasta file with about 5800 lncRNAs found on F. vesca and I would like to map them in a reference genome. Which software should I employ? I don't know if HISAT or STAR could work with sequences of that length.
I would suggest using minimap2 or GMAP for this task since both can do spliced alignment of long reads/fragments. Even if the reads are not entirely incorrect you should get nice results. Those tools also work with error-prone nanopore and Pacbio transcriptome sequencing.