FLIC - Full-Length Isoform Constructor
Advances in high-throughput sequencing have illuminated a complexity of transcriptome landscape in eukaryotes. An inherent part of this complexity is the presence of multiple isoforms generated by the alternative splicing and the use of alternative transcription start and polyadenylation sites. We developed FLIC (Full-Length Isoform Constructor) - a hybrid pipeline which combines the information on splice sites inferred from short-read data with the information on their ordering based on long reads. A direct comparison shows that FLIC is as accurate as CAGE, currently regarded as a golden standard for TSS identification, while being much less time-consuming.FLIC and a set of accompanying scripts for cDNA analysis are available at: https://github.com/albidgy/FLIC.Overall design: Arabidopsis thaliana mature rosette leaves were harvested, and modified protocol of barcoded cDNA libraries construction for Oxford Nanopore Sequencing was applied. CAGE libraries were constructed starting with the same RNA.