
==== Front
bioRxiv
BIORXIV
bioRxiv
2692-8205
Cold Spring Harbor Laboratory

39229095
10.1101/2024.08.23.609463
preprint
2
Article
SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments.
Keil Netanya
Monzó Carolina
McIntyre Lauren http://orcid.org/0000-0002-0077-3359

Conesa Ana
17 9 2024
2024.08.23.609463https://creativecommons.org/licenses/by-nc-nd/4.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
http://biorxiv.org/lookup/doi/10.1101/2024.08.23.609463
nihpp-2024.08.23.609463.pdf
SQANTI-reads leverages SQANTI3, a tool for the analysis of the quality of transcript models, to develop a quality control protocol for replicated long-read RNA-seq experiments. The number/distribution of reads, as well as the number/distribution of unique junction chains (transcript splicing patterns), in SQANTI3 structural categories are compiled. Multi-sample visualizations of QC metrics can also be separated by experimental design factors. We introduce new metrics for 1) the identification of potentially under-annotated genes and putative novel transcripts and 2) variation in junction donors and acceptors. All scripts are open source and customizable. Using two different datasets, one from Drosophila and one benchmark dataset from the LRGASP project, we demonstrate how low coverage does not automatically indicate low quality and how strong/weak splicing sites can be readily identified genome wide. SQANTI-reads is open source and available for download at GitHub.
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pmc
