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. The advantages of this approach include: * easy detection of novel introns * modeling of more complex splicing events than exonic PSI * avoiding the challenge of isoform abundance estimation * simple, computationally efficient algorithms scaling to 100s or even 1000s of samples
Environment Modules¶
Run module spider leafcutter to find out what environment modules are available for this application.
Environment Variables¶
- HPC_LEAFCUTTER_DIR - installation directory
- HPC_LEAFCUTTER_BIN - executable directory
- HPC_LEAFCUTTER_GIT - github repository
Categories¶
biology, sequencing