Long-read Isoform Quantification and Analysis

LIQA (Long-read Isoform Quantification and Analysis) is an Expectation-Maximization based statistical method to quantify isoform expression and detect differential alternative splicing (DAS) events using long-read RNA-seq data. LIQA incorporates base-pair quality score and isoform-specific read length information to assign different weights across reads instead of summarizing isoform-specific read counts directly. Moreover, LIQA can detect DAS events between conditions using isoform usage estimates.

Computational pipeline of LIQA

<p align="center"> <img width="575" height="406" src="doc/liqa_flowchart.png"> </p>

Inputs of LIQA

The input of LIQA is long-read RNA-seq read data in BAM format together with a reference isoform annotation file.

Installation

Please refer to Installation for how to install LIQA.

Usage

Please refere to Usage for how to use LIQA.

Examples of isoform analysis using LIQA.

Please refer to Tutorial and FAQs for a tutorial of LIQA with the example data along with FAQs.

Contact

If you have any questions/issues/bugs, please post them on GitHub. They would also be helpful to other users.

Citation

Hu, Y., Fang, L., Chen, X. et al. LIQA: long-read isoform quantification and analysis. Genome Biol 22, 182 (2021). https://doi.org/10.1186/s13059-021-02399-8