multiple entries with the same exon_number for a given transcript_id

[zhangkn3]

Hi Andre, Thanks for your great contribution to the Bambu pipeline. I am running it to identify novel transcripts from long-read sequencing data.

However, I found multiple entries with the same exon_number for a given transcript_id in the gtf output.

This is one of them. How should I understand the output?

Looking forward to hearing from you!

Best, Kenan

[andredsim]

Hi Kenan,

Sorry for the late response. The exon number is the the index of the exon within that particular transcript from 1 to n (n is the number of exons). There would be a problem is the same transcript id had multiple of the same exon number but I cannot seem to see that in the example unless I have overlooked it.

Let me know if this has cleared it up, or if I misunderstood the issue.

Kind Regards, Andre Sim