Welcome to LongPolyASE documentation

This is the documentation for LongPolyASE, a framework for allele-specific expression analysis using long-read RNA-seq and phased genome assemblies.

The framework consists of three components:

Flowchart of the polyase framework

  1. syntelogfinder: a nextflow pipeline to identify syntenic genes in phased genome assemblies using GENESPACE. Input: phased genome assembly and their annotations in GFF3 format.

  2. longrnaseq: a nextflow pipeline for allelic gene and isoform quantification of long-read RNA-seq data, including novel isoform discovery and quality control. Input: long-read RNA-seq data (PacBio or ONT)(2 conditions and replicates) and a phased genome assembly with its annotation in GTF format.

  3. polyase: a python package for allele-specific expression analysis using the inputs of the two previous components. Gene and isoform-level ASE analysis, differential isoform usage analysis, and visualization of the results. Input: the outputs of syntelogfinder and longrnaseq.

Getting Started:

Tutorial:

API Reference:

Indices and tables