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:

Merge_htseq_count-1.0 app is used for combining the count files generated from apps such as Htseq-count or Featurecount into one table. The Htseq-count and Featurecount apps produce raw counts for individual samples and it is necessary to combine them into a single table for downstream analysis such as differential gene expression using DESeq2 or edgeR etc.,

Merge_htseq_count-1.0 is invoked using the following:

  1. Input (s)
    1. Directory containing the count files from either Htseq-count or Featurecount
    2. Output file name (Default is Output_file.txt)

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

 The test data for Merge_htseq_count-1.0 consists of 6 count files generated from Htseq-count-0.61 app

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All files are located in the Community Data directory of the iPlant Discovery Environment at the following path: Community Data > iplantcollaborative > example_data > Merge_htseq-count (/iplant/home/shared/iplantcollaborative/example_data/Merge_htseq-count/)

Run SplAdder as following:

  1. Input (s)
    1. The folder containing the list of alignment files - /iplant/home/shared/iplantcollaborative/example_data/Merge_htseq-count/
    2. Output file name (Default is Output_file.txt)