The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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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
  3. Directory of ctab files from stringtie output
 
  1. 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.

Test Data

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
  3. Directory of ctab files from stringtie output
    1. StringTie-1.3.3_from_merged_annotation/ballgown_input_files

Output:

Successful execution of Ballgown-2.0 generates the following outputs:

Image Added

  • 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:

Tool Source for App

https://www.bioconductor.org/packages/release/bioc/html/ballgown.html