Calculate PSI in gtf files in python

Question

[H1LLCH1NG]

Hi, I've search many posts about calculating PSI(percentage of spliced in), their first step are all process the BAM file. And I just want to calculate the PSI of exon in reference file (gencode.v39.chr_patch_hapl_scaff.annotation.gtf). Anyone would tell me how can I calculate PSI ?

Answer 1

[benformatics]

This kind of analysis is not super straightforward as you have to have your splice junction annotations well defined for the calculations.

If you are using R, I prefer: http://rnaseq-mats.sourceforge.net/

There is also a python based options https://miso.readthedocs.io/en/fastmiso/

you could dig around here: https://github.com/yarden/MISO