sj2psi | Convert RNA-STAR aligner

sj2psi is a Python library. sj2psi has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

Annotation-free estimation of percent spliced in of a junction. This will convert [RNA-STAR aligner] "SJ.out.tab" files to "Percent spliced-in" (Psi) scores. Here’s an example of an SJ.out.tab file:. As described in [Pervouchine et al, Bioinformatics (2013)] we will take the approach of asking, how often is this donor site (5' splice site) used with this acceptor site (3' splice site), compared to ALL OTHER acceptors?. Same goes for acceptor sites. How often is this acceptor site, used with this donor site, compared to ALL OTHER donors?. To illustrate, check out this example. Each "-" represents 10 bp. For the 5' splice site chr1:100, we have 90+10 = 100 total reads. Thus the "psi5" for chr1:100-180 is 90/100 = 0.9, and 0.1 for chr:100-200. For the 3' splice site chr1:200, we have 10+40 = 50 total reads. Thus the "psi3" for chr1:100-200 is 10/50 = 0.2, and 0.8 for chr:130-200. What’s left is the uninteresting splice sites of chr1:180 and chr1:130, both of which didn’t have any variance and were always used. Thus psi3 for chr1:180 is 1.0, and psi5 for chr1:130 is 1.0 as well.