Inclusion_list.tsv and rescue_table.tsv mismatch issue

[ljh-9809]

Hello, I have encountered an issue in SQANTI3 where the isoform entries between inclusion_list.tsv and rescue_table.tsv do not match as expected. For some isoforms, inclusion_list.tsv contains entries that do not appear in rescue_table.tsv, and vice versa. Could you provide clarification on why this mismatch occurs and how to resolve or interpret it? Is this expected behavior, or does it indicate a problem with the pipeline? Thank you.

[pabloati]

Hi, we experienced that issue in the past. Are you running SQANTI3 in its latest release? If yes, I would appreciate if you could send me some data to reproduce the issue.

Best,
Pablo