Calculating relative exon inclusion (percent spliced in = PSI) values for a single BAM file

[Sam Harvey]

Hello rMATS Community,

I am interested in finding the best tool to calculate the splicing signature of single BAM files. I am wondering, is it possible to run rMATS providing a single BAM file and associated annotation file to obtain the percent spliced in (PSI) values for every variable exon. At this point, I do not want rMATS to determine the differential splicing between multiple samples.

If rMATS does not provide this functionality, are you aware of another tool that does?

Thank you for your time. I apologize if this question has already been answered, but I wasn't able to find it after a couple forum searches.

Sincerely,

Sam

[Juw Won Park]

Hello,

It's not recommended but you can use the same files for sample_1 and sample_2. You will not find any significant AS events but you will get the PSI estimates for each event.

-Juw Won

[Sam Harvey]

Thank you, Juw Won. I will consider this option if I can't figure out a better way to get PSI estimates for a single sample.

Thanks,

Sam