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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Rationale


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 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:

  • 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

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