Ballgown Differential Transcript Expression Output Table

Question

[galaxy]

Hello everyone,

I was wondering if anybody could help me understand the output I am getting using the StringTie --> Ballgown pipeline in order to measure differential transcript expression between two groups. My confusion some of the column name identifiers that the ballgown uses. Mainly, "transcriptNames", "id" and "geneIDs". Could anyone help me to understand the difference between these 3 things? I have posted a snnipet of the table below if it helps. I greatly appreciate your time and expertise.

[Ram]

Relevant thread for MSTRG geneIDs: How to deal with MSTRG tag without relevant gene name?

transcriptNames are the NCBI transcript identifiers. id seems to be an auto-incrementing identifier. Of these columns, it looks like only the geneNames and transcriptNames can be used to link to external databases using tools like biomaRt.

[galaxy]

I greatly appreciate your reply. This is very helpful!