Best-guessing insert size and stddev in MISO using paired-end data versus running MISO single ended

Question

[floris.barthel]

I am conducting a miso analysis for a single gene on a large number of Paired End RNAseq bams that is spread out on several external HDs (twenty 4tb drives). Computing insert sizes for these is extremely tedious and slow. However, running MISO itself (in single-end mode or paired end mode with best guess insert sizes) for a single gene runs extremely fast. Because of the speed, calculating exact insert sizes is not an option. For several samples, the mean insert size is around 150-250 and the stddev is more or less 50. Therefore, in my opinion I have two options:

1. Run miso in single-end mode
2. Run miso in paired-end mode and best guessing insert size at 250 and sd at 50

I wonder if option 2) may be superior because the data is paired end. Can anyone comment on their thoughts? Would be extremely helpful.