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.
The input of LIQA is long-read RNA-seq read data in BAM format together with a refrence isoform annotation file.
Please refer to Installation for how to install LIQA.
Please refere to Usage for how to use LIQA.
Please refer to Tutorial and FAQs for a tutorial of LIQA with the example data along with FAQs.
If you have any questions/issues/bugs, please post them on GitHub. They would also be helpful to other users.
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