Recommended workflow for RNA long read Kallisto-like TPM estimation? On short reads, Kallisto/Salmon is a standard workflow for measuring RNA transcript counts in TPM. However, when I tried to Google a similar workflow for long reads, it's not clear there is a replacement.
Stringtie now does long reads too. We've found flair to be quite difficult to install and to crash often. That said, stringtie isn't very good about showing you its working (e.g. I have no idea how to get it to give the assembly it uses to figure out all the isoforms). Its values for TPM/FPKM also seem a little weird, in that they're perfectly correlated with each other, and for transcripts they're perfectly correlated with coverage too.
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1910-1
https://github.com/gpertea/stringtie
TALON is another tool that does isoform assembly. I'm not sure whether it does quantification though.
https://github.com/mortazavilab/TALON#