A statistical tool to quantify isoform-specific expression using long-read RNA-seq
Project description
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
Inputs of LIQA
The input of LIQA is long-read RNA-seq read data in BAM format together with a refrence isoform annotation file.
Installation
Please refer to Installation for how to install LIQA.
Usage
Please refere to Usage for how to use LIQA.
Contact
If you have any questions/issues/bugs, please post them on GitHub. They would also be helpful to other users.
Citation
Yu Hu, Li Fang, Xuelian Chen, Jiang F. Zhong, Mingyao Li, Kai Wang. LIQA: Long-read Isoform Quantification and Analysis. 2020. bioRxiv doi: https://doi.org/10.1101/2020.09.09.289793
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