Alternative Splicing

Alternative splicing is a fundamental cellular mechanism with a significant impact on regulatory processes and gene products. During this process, the exons of a transcript are partially skipped or rearranged. This process is mediated by the spliceosome.

The following describes a program developed for the quantification of skipped exon events. Its results are evaluated using a hypothesis test. The program was run on ten bam files using annotation_b37.gtf as the reference genome. Additionally, the results are compared to a previously published tool (DEXSeq, from Anders et al., 2012).

Usage

java -jar psi.jar -bam <bam> 
                  -gtf <gtf> 
                  -o <out.psi>

Logic

Figure created using BioRender (BioRender, 2024).

Percent Spliced-In Value

$$ PSI := \frac{IRC}{IRC + ERC} $$

Where IRC are inclusion read counts and ERC are excluding read counts.