Intron retention gene expression using salmon

Question

[shinyjj]

I have a list of intron retention found in my short read data. I want to see if those intron retentions are lowly expressed. Can somebody comment on my experiment step if this is correct?

1. Run my data (bam file) using salmon
2. Sum up the TPM level of the same transcripts that contain intron retentions
3. Check the distribution of TPM level that contains intron retentions using boxplot

Another question popped up in my head is that are there any tools to quantify gene expression like salmon using long read data as well?