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sQTL

THISTLE

  • SHORT NAME: THISTLE
  • FULL NAME:testing for heterogeneity between isoform-eQTL effects
  • DESCRIPTION:THISTLE (testing for heterogeneity between isoform-eQTL effects) is a transcript-based splicing QTL (sQTL) mapping method that uses either individual-level genotype and RNA-seq data or summary-level isoform-eQTL data.
  • URL : https://yanglab.westlake.edu.cn/software/osca/#THISTLE
  • CITATION:Qi, T., Wu, Y., Fang, H. et al. Genetic control of RNA splicing and its distinct role in complex trait variation. Nat Genet 54, 1355–1363 (2022). https://doi.org/10.1038/s41588-022-01154-4

sQTLseekeR

  • SHORT NAME: sQTLseekeR
  • FULL NAME: sQTLseekeR
  • DESCRIPTION:sQTLseekeR is a R package to detect splicing QTLs (sQTLs), which are variants associated with change in the splicing pattern of a gene. Here, splicing patterns are modeled by the relative expression of the transcripts of a gene.
  • URL :https://github.com/jmonlong/sQTLseekeR
  • CITATION: Monlong, J., Calvo, M., Ferreira, P. et al. Identification of genetic variants associated with alternative splicing using sQTLseekeR. Nat Commun 5, 4698 (2014). https://doi.org/10.1038/ncomms5698

LeafCutter

  • SHORT NAME: LeafCutter
  • FULL NAME:LeafCutter
  • DESCRIPTION: Leafcutter quantifies RNA splicing variation using short-read RNA-seq data. The core idea is to leverage spliced reads (reads that span an intron) to quantify (differential) intron usage across samples.
  • URL : https://davidaknowles.github.io/leafcutter/
  • CITATION:Li, Y.I., Knowles, D.A., Humphrey, J. et al. Annotation-free quantification of RNA splicing using LeafCutter. Nat Genet 50, 151–158 (2018). https://doi.org/10.1038/s41588-017-0004-9