Dear authors,

Thank you for a great tool and efforts to maintain it!

I recently ran IsoQuant on my bulk long-read PacBio data, but I do not see the header row in .novel_vs_known.SQANTI-like.tsv. According to #202 , this file is similar but not the same as SQANTI-output, listed in _classification.txt in SQANTI output format. Would you know if there is anything I can do to fix the header row?

Also, I see there are 28 full_splice_match transcripts in this file, which has 113,775 entries in total. Would these just be some novel transcripts highly similar to annotated ones?

Thank you so much for your time!

Below is a part of my isoquant.log showing the versions:

2025-06-18 14:42:48,350 - INFO - Running IsoQuant version 3.7.0
2025-06-18 14:42:48,350 - WARNING - Output folder already exists, some files may be overwritten.
2025-06-18 14:42:48,362 - INFO -  === IsoQuant pipeline started === 
2025-06-18 14:42:48,362 - INFO - Python version: 3.8.20 | packaged by conda-forge | (default, Sep 30 2024, 17:52:49) 
[GCC 13.3.0]
2025-06-18 14:42:48,362 - INFO - gffutils version: 0.13
2025-06-18 14:42:48,362 - INFO - pysam version: 0.22.1
2025-06-18 14:42:48,362 - INFO - pyfaidx version: 0.8.1.4