I am working on RNA-Seq data analysis. I am following the new tuxedo pipeline as per protocol. I have successfully processed my files using HISAT2 and StringTie on the Galaxy server. The output of StringTie gives a .gtf file and .tabular file. I have not done StringTie merge. Next, I want to do differential gene expression using Ballgown on R. But the ballgown software requires .ctab files as input, which I do not have. Is . tabular file same as .ctab format? Please help me with this as to how the output of StringTie is supposed to be used as input for ballgown. What parameters are to be given while running StringTie on Galaxy to produce the desired output format for ballgown?
Any help will be much appreciated as I’m on my last stage of analysis.
Good morning, Lakshmi,
The flag for ballgown output, if StringTie is a recent enough version, is -B. Newer Galaxy wrappers should also support this flag.
Thanks for the response!
Also, I am using the Galaxy server online for using HISAT2 and StringTie tools.
Can you tell whether it’s on terminal or Galaxy server?