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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HTProcess_fastqc-0.1

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First of a series of interrelated tools for processing data by library, rather than by individual files.

Quick Start

  • To use HTProcess_fastqc-0.1, import your files in fastq format. The HTProcess set of Apps is designed to take in a well-defined library of reads and run fastqc on each, and to test the pairing of paired reads. Paired reads are entered in 2 separate directories for left and right read files. The unpaired read files are entered in a third separate directory. For the ease of drag and drop entry of the individual files, use the DE Workflow, HTProcess-Prepare_directories-and-run_fastqc-0.1. HTProcess_fastqc-0.1 and the Workflow version also create a manifest file, which enters important information about the read library being analysed and records it in a format that can be read automatically in downstream HTProcess Apps. 
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  • *Additional Resources: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/*

Test Data

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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> htprocess1 ->sample_input_files ->.

Input File(s)

This App is designed to take only folders of reads as input. Use the folders forward_reads, reverse_reads, and singles from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

Use the following sample settings to achieve the same results as given in the example_data section:

    • library name - testfiles
    • library number or second name - 1
    • library condition - testing
    • Paired End Spacing - 400
    • Standard Deviation for Paired End Spacing - 35
    • Type of Paired Reads - fragment

Output File(s)

Expect a folder named HTProcess_Reads as output, as well as the fastqc_summary.html file. The folder is ready to use with HTProcess-Trimmomatic, for example, for a next step.

The fastqc_summary.html file provides a table of graphical outputs from running fastqc with the input read files. It can be read directly in your browser by clicking on it in the DE. An example of the output for the sample data is given under Community Data -> iplantcollaborative -> example_data -> htprocess1 -> HTProcess_fastqc .

Tool Source for App

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