"Transcripts missing gene assignment in annotation file" error

[joelnitta]

I get the "Transcripts missing gene assignment in annotation file" warning when creating my project, even though those transcript IDs are in the GFF3 file. I am using a custom GFF3 file. I ran into this once and was able to fix almost all of the missing transcripts by sorting the matrix data file in numeric order of transcript ID; at first >20,000 transcripts were reported as "missing", and after sorting it is down to 6. However, I can't figure out why it thinks those 6 are missing.

I would be happy to share my data via email if that would help.

tappas v1.0.7 on mac OS 13.1

[almart7]

Hello @joelnitta, sorry for the late reply. Please send me your data (also the GFF3 file) so I can take a look on it.