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sid-sethi merged 1 commit into from
Jan 6, 2026
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updating psqan's citation #6

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10 changes: 9 additions & 1 deletion README.md
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Expand Up @@ -29,10 +29,13 @@
- [Ranked transcripts](#ranked-transcripts)
- [Other useful commands](#other-useful-commands)
- [Licence](#licence)
- [Citing PSQAN](#citing-psqan)

## Overview
<img src="images/figure_for_github.png" width="870" height="750"/>

> **_Publication:_** *Bioinformatics Advances (2025)*. DOI: https://doi.org/10.1093/bioadv/vbaf293

## Introduction
Despite the advances in tools to process long-read RNA-sequencing (lrRNA-seq) data, the downstream analysis of transcriptional data remains challenging due to the detection of thousands of novel transcripts and the lack of tools to prioritise functionally important transcripts. From such a large number of transcripts, it is difficult to distinguish between stable transcripts of potential biological importance, partially processed RNAs and splicing noise. Furthermore, when using lrRNA-seq to identify rare and novel transcripts, the recommendation is to incorporate multiple replicates in the study design and implement transcript-level filters. However, determining optimal expression thresholds for filtering and selecting transcripts which are reproducible across samples remains a significant challenge. Consequently, researchers find it challenging to interpret lrRNA-seq data effectively and generate relevant hypothesis which could be experimentally validated in the laboratory.

Expand Down Expand Up @@ -237,4 +240,9 @@ Copyright 2024 Astex Therapeutics Ltd.

This repository is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the [LICENSE](LICENSE) file (GNU General Public License) for more details.
This repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the [LICENSE](LICENSE) file (GNU General Public License) for more details.

## Citing PSQAN
If you use PSQAN in your research, please cite the following publication: https://doi.org/10.1093/bioadv/vbaf293

Siddharth Sethi, Emil K Gustavsson, Harpreet Saini, Mina Ryten, PSQAN: a pipeline to prioritize novel and biologically relevant transcripts from long-read RNA sequencing, Bioinformatics Advances, Volume 5, Issue 1, 2025, vbaf293, https://doi.org/10.1093/bioadv/vbaf293