Questions Regarding Using StringTie for DRS Data Analysis

[Taylorain]

Hello, I’m using StringTie to process my Direct RNA Sequencing (DRS) data, and I have a few questions regarding the usage of certain parameters. Below is the command I used:

stringtie /5.1_merge/all.merged.sorted.bam -o stringtie.gtf -R -p 150 -u --conservative -L  

Based on the output generated, I have the following concerns:

1. Regarding the -R parameter: Could you provide more details on how this parameter should be used and the scenarios where it is most applicable?
2. Considering DRS data: Since DRS involves full-length RNA sequencing without fragmentation, are there any improvements or adjustments I could make to my command to optimize the analysis? For instance, should I modify the -m parameter?
3. Isoform support threshold: I would like to ensure that each isoform is supported by at least three reads. What parameters should I adjust during the collapsing step to enforce this threshold?

Thank you in advance for your guidance. Your help is greatly appreciated! Best regards,