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:

1. experiment design matrix file
   
   

   1. A file containing SRA ids (1 SRA id per line)

2. experimental covariate of interest
   
   

   1.  The experimental covariate of interest (For example - "condition")

3. Directory of ctab files from stringtie output 

   1. 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 support@cyverse.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)

 Run Ballgown-2.0 as following:

1. experiment design matrix file
   
   

   1. design_matrix

2. experimental covariate of interest
   
   

   1. condition

3. Directory of ctab files from stringtie output
   
   

   1. StringTie-1.3.3_from_merged_annotation/ballgown_input_files

Successful execution of Ballgown-2.0 generates the following outputs:

Open

• DE_plot.pdf:

• FPKM_boxplot.pdf:

• Histogram_number_transcripts_gene.pdf:

• Histogram_transcript_sizes.pdf:

• MA_plot.pdf:

• MDS_plot.pdf:

• results_gene.tsv:

• results_gene_filter.sig.tsv:

• results_gene_filter.tsv:

• results_trans.tsv:

• results_trans_filter.sig.tsv:

• results_trans_filter.tsv: