<div dir="ltr">Hello,<div><br></div><div>I was able to execute run_events_analysis.py on my BAM file without errors, but the resulting output directory does not contain any Psi values (no .miso files). If I then summarize the output with run_miso.py (again with no errors occurring) I get a summary file (.miso_summary) with the header information but no events (consistent with the output of run_miso.py which gives "Summarized a total of 0 events").</div>
<div><br></div><div>It seems that MISO is working properly and I've given it the appropriate files (BAM, index file, indexed GFF, etc.).</div><div><br></div><div>Since the issue could be with my specific GFF annotation or the BAM file itself, I was wondering how I could diagnose this problem. Is there a small sample dataset I can use to verify that MISO is working correctly? My GFF should contain the appropriate isoform information, and I find it very unlikely that the 3321783 paired mates in my BAM file don't have expression of the isoforms present in my GFF.</div>
<div><br></div><div>Any ideas? I would be very grateful for any help!</div></div>