StringTie output as Ballgown input
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lakshmi9c • 0
@lakshmi9c-23931
Last seen 3.9 years ago

Hello, I am working on RNA-Seq data analysis. I am following the new tuxedo pipeline as per Pertea 2016 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. Thanks!

ballgown StringTie galaxy rnaseq • 1.6k views
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Kevin Blighe ★ 4.0k
@kevin
Last seen 4 weeks ago
Republic of Ireland

Hi there, this question is not related to any Bioconductor package. You should post this question on Biostars or, preferably, the Galaxy support forum: https://help.galaxyproject.org/

Kevin

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Isn't Ballgown a Bioconductor package ?

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Yes, henry-keen; however, please note the following quotes:

I have successfully processed my files using HISAT2 and StringTie on the Galaxy server.

What parameters are to be given while running StringTie on Galaxy to produce the desired output format for Ballgown?

Kevin

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