Developed for analysing short-read RNA-Seq data, existing tools for assessing alternative splicing events fail to capture the connectivity and complexity of isoforms detected from long-read sequencing, particularly those generated from targeted profiling where a deep sequencing coverage is achieved.
FICLE (Full Isoform Characterisation from Long-read sequencing Experiments) is a tool subsequently developed to comprehensively annotate and accurately document the full reportoire of isoforms identifed from targeted full-length long-read sequencing experiment. It accurately assesses the occurrence of alternative splicing events by comparing splice sites (exon) coordinates between long-read-derived transcripts and reference transcripts, further easing visualisation of isoforms on the UCSC genome browser.
Please see the Wiki page for more details:
SK.Leung, A.R.Jeffries,...E.Hannon, J.Mill. Long-read transcript sequencing identifies differential isoform expression in the entorhinal cortex in a transgenic model of tau pathology. doi: https://doi.org/10.1101/2023.09.20.558220