Differential gene expression anaylsis -Ballgown

Question

[amy16]

Hi, Can the output from stringtie (transout.gtf, .ctab files) be used directly for accessing the assembly data or does it have to pass through the match assembled transcripts to annotated transcripts?

-Thanks in advance

[Kristoffer Vitting-Seerup]

Only if you want to annotate the transcript to actually know which genes they belong to

Answer 1

[Hussain Ather]

They can be accessed directly with Ballgown or cufflinks.