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                                            Rhopala

Question about applying PCA on intron usage ratios

Dear leafcutter team, The [splicing QTL vignette](https://davidaknowles.github.io/leafcutter/articles/sQTL.html) uses the `prepare_phenotype_table.py` to prepare association analysis data, including performing PCA on intron usage ratios to generate hidden covariates. However, since hidden covariates...

Confusion about Proper Input File Extension and Content

Greetings! We are using LeafCutter on splicingQTL analysis and had some confusion on input file structures. We have two aligned .bam files from our previous steps: one with extension Aligned.toTranscriptome.out.bam...