A schematic diagram of IsoSplitter design. IsoSplittingAnchor determines the split sites of transcripts through selection using a modified SIM4 algorithm; the default parameters for HSP selection are shown and can be customized. Transcriptome sequences after removing redundancy from long-read sequencing are recommended Input files; other transcriptome collections that contain extensive gene alternative splicing isoforms are suitable for the analysis as well. When short RNA-seq reads are available, ShortReadsAligner maps the short reads and identifies junction reads and isoform-specific reads that validate and quantify the split sites. Finally, isoform expression levels are calculated based on sequence reads. Red boxes indicate output files. The prediction of AS isoforms is supported by the junction reads; and to reveal the tissue-specific expression of isoforms the isoform-specific reads are calculated into ACM for quantification. The stars indicate the split sites identified by the SIM4 alignments.
