Intron offset miscalulated

[Mansi Dalal]

I am encountering several warnings related to miscalculated intron offsets while running intron retention detection on my BAM file using MAJIQ. The log outputs show messages like:  

Intron offset 1238 miscalculated 

Intron offset 777 miscalculated 

Intron offset 732 miscalculated  

2025-05-03 13:35:17,340 (PID:9218) - INFO - Reading bam file /home/2_1.bam 2025-05-03 13:36:05,843 (PID:9218) - INFO - Detect Intron retention 2_1 Intron offset 4480 miscalculated  

Could you please clarify what these “intron offset miscalculated” warnings indicate? Do they suggest a compatibility issue with the annotation file, or are they safe to ignore? If action is needed, I would appreciate guidance on how to resolve or mitigate these warnings.  

[San Jewell]

Hello,

The exact anomaly in certain BAM files which causes this message is not yet fully understood. The lab has a task to resolve it for v2. However, it is notable that each line this message is put out, it only means that one read could not be placed. The majority of your analysis should be unaffected. (For example, in this case, there will be three intron reads that could not be placed in the entire run, which is usually a vanishingly small part of total reads)

Thanks,

-San