Scholarlink

<p>Advancements in high-throughput sequencing have revolutionized transcriptomics, enabling insights into gene expression, splicing, and fusions. However, RNA-seq analysis remains challenging due to complex splice junctions, multi-mapped reads, and chimeric events. We present DeepSAP, which improves RNA-seq alignment by integrating GSNAP’s transcriptome-guided genomic alignment with transformer-based splice-junction scoring. This synergy enhances splice-junction detection, indel identification, and resolution of complex splicing patterns. On the Baruzzo human simulated benchmark across complexities, DeepSAP achieves the highest mean F1-score for splice junction detection, outperforming DRAGEN, novoSplice, STAR, HISAT2, and Subjunc. DeepSAP captures intricate sequence patterns surrounding splice donor and acceptor sites, advancing RNA-seq analysis.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

DeepSAP: improved RNA-seq alignment by integrating transcriptome guidance with transformer-based splice junction scoring

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年5月9日

查看全文
  • Fadel Berakdar,
  • Thomas D. Wu,
  • Tong Zhu,
  • Mehrzad Samadi,
  • Pankaj Vats

摘要

Advancements in high-throughput sequencing have revolutionized transcriptomics, enabling insights into gene expression, splicing, and fusions. However, RNA-seq analysis remains challenging due to complex splice junctions, multi-mapped reads, and chimeric events. We present DeepSAP, which improves RNA-seq alignment by integrating GSNAP’s transcriptome-guided genomic alignment with transformer-based splice-junction scoring. This synergy enhances splice-junction detection, indel identification, and resolution of complex splicing patterns. On the Baruzzo human simulated benchmark across complexities, DeepSAP achieves the highest mean F1-score for splice junction detection, outperforming DRAGEN, novoSplice, STAR, HISAT2, and Subjunc. DeepSAP captures intricate sequence patterns surrounding splice donor and acceptor sites, advancing RNA-seq analysis.