Ballgown is a R library written for RNAseq data analysis as part of New tuxedo workflow. For this, you should have followed the note here on RNAseq analysis. Ballgown library in R allows the user to download the output from StringTie and allows the user to do statistical analysis.
Ballgown-2.0 is invoked using the following:
experiment design matrix file
A file containing SRA ids (1 SRA id per line)
experimental covariate of interest
Directory of ctab files from stringtie output
Output from StringTie is present in 6 directories under stringtie folder
Please work through the documentation and add your comments on the bottom of this page, or email comments to firstname.lastname@example.org. Thank you.
All files are located in the Community Data directory of the CyVerse Discovery Environment at the following path:
Community Data > iplantcollaborative > example_data > HISAT2-StringTie-Ballgown (/iplant/home/shared/iplantcollaborative/example_data/HISAT2-StringTie-Ballgown)