sQTLseekeR2

sQTLseekeR2 is an enhanced version of sQTLseekeR, an R package to detect splicing QTLs (sQTLs).

Installation

From R:

install.packages("devtools")
devtools::install_github("guigolab/sQTLseekeR2")

R 3.3 or higher is required.

Enhancements

• Covariate correction
• Faster pre-processing of transcript expression
• Improved P-value calculation with higher precision
• Permutation-based schema for multiple testing correction
• LD-based variant clustering

Analysis steps

• Index the genotype file. index.genotype compresses and indexes the genotype file to optimize the access to particular regions.

• Preprocess the transcript expression data. prepare.trans.exp removes transcripts with low expression and genes expressing only one transcript, with low splicing dispersion, with few different splicing patterns or low expression. Then relative transcript expression is computed.

• Test for association between splicing ratios and genetic variants in cis (nominal pass). sqtl.seeker computes a nominal P-value for each variant-gene pair, testing for the association between the genotype and the transcript relative expression.

• Obtain an empirical P-value for each phenotype (permutation pass, optional). sqtl.seeker.p implements a permutation scheme that empirically characterizes, for each gene, the distribution of nominal P-values expected under the null hypothesis of no association. This null distribution is then modeled using a beta distribution as in FastQTL.

• Control for multiple testing. sqtls computes FDR (Benjamini-Hochberg's or Storey's) across all nominal tests. Alternatively, if sqtl.seeker.p has been run, sqtls.p performs FDR on empirical P-values and then, to recover all significant variant-gene pairs, implements a procedure identical to the one depicted here.

For additional information on the analysis steps you can have a look at sQTLseekeR.

Running sQTLseekeR2 on computing clusters (recommended)

sQTLseekeR2 can be easily used on a cluster thanks to Nextflow. See sqtlseeker2-nf for details.

Cite sQTLseekeR2

If you find sQTLseekeR2 useful in your research please cite the related publication:

Garrido-Martín, D., Borsari, B., Calvo, M., Reverter, F., Guigó, R. Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome. Nat Commun 12, 727 (2021). https://doi.org/10.1038/s41467-020-20578-2