Pipeline to convert long-read sequencing data to a representative transcriptome for a cancer type and perform primary sequence characterization of the novel ORFs. The flowchart of the pipeline is shown here:
000_ccs2gtf.sh: This script converted raw data from the Pacbio sequencer to the master transcriptome.
001_gtf2orf.sh: This script performed QC, predicted the ORFs, and performed primary sequence characterisation of the master transcriptome.
002_gtf2qnt.sh: This script performed quantification of the master transcriptome based on external short-read RNA-seq datasets.
003_orf2ms.sh: This script performed MS/MS validation of predicted novel ORFs.