Figure 4.

Analysis challenges of long-read full-length sequencing. A simplified schematic shows the steps required to extract information out of long-read sequencing data. Each read has to be aligned, ideally in a allele-aware manner to the genome it originated from. Read alignments then have to be analysed to identify RNA modifications as well as new isoform features that are missing in the current transcriptome annotation. For each allele, reads then have to be grouped into isoforms which allows isoform identification and quantification. For real datasets, all these steps have to take into account the often substantial rates of sequencing errors and incomplete reads in long-read sequencing. These will complicate all steps of the analysis.