isoseq2orf Pipeline

isoseq2orf is a pipeline designed to convert long-read sequencing data into a representative transcriptome for a specific cancer type and perform primary sequence characterization of novel open reading frames (ORFs).
The workflow of the pipeline is illustrated below:

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📌 Pipeline Overview

The pipeline consists of the following key steps:

1. Convert raw sequencing data (000_ccs2gtf.sh)
2. Predict ORFs and perform quality control (001_gtf2orf.sh)
3. Quantify the master transcriptome using short-read RNA-seq (002_gtf2qnt.sh)
4. Validate predicted ORFs using MS/MS (003_orf2ms.sh)

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🛠 Pipeline Scripts

1️⃣ 000_ccs2gtf.sh

Function:
🔹 Converts raw data from the PacBio sequencer into the master transcriptome.

2️⃣ 001_gtf2orf.sh

Function:
🔹 Performs quality control (QC).
🔹 Predicts open reading frames (ORFs).
🔹 Conducts primary sequence characterization of the master transcriptome.

3️⃣ 002_gtf2qnt.sh

Function:
🔹 Quantifies the master transcriptome based on external short-read RNA-seq datasets.

4️⃣ 003_orf2ms.sh

Function:
🔹 Performs MS/MS validation of the predicted novel ORFs.

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This pipeline enables comprehensive analysis of novel ORFs derived from long-read sequencing, integrating transcriptomic, proteomic, and functional data.