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-prepare_directories-and-run_fastqc-0.1

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HTProcess workflow to run HTProcess-prepare-input-directories and HTProcess-fastqc. Takes individual files as input and initializes a library of reads for analysis via the HTProcess-workflow, and runs fastqc on all files.

Quick Start

Test Data

Icon

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

Input File(s)

Use all the fastq files 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.

Library_name=Belgica_genome
Library_num=1
condition=control
pairing=paired_and_unpaired
pair_spacing=300
pair_sd=35
pair_type=fragment
Library_name=Belgica_genome

Library_num=1

condition=control

pairing=paired_and_unpaired

pair_spacing=300

pair_sd=35

pair_type=fragment

Outputs

The expected output includes all the files found here (except for the Input_Files):

Community Data -> iplantcollaborative -> example_data -> htprocess1 -> HTProcess_fastqc -> 

The main output is the HTProcess_Reads directory which is ready to use as input with HTProcess_trimmomatic. The other file of specific interest is fastqc_summary.html, which can be clicked on to open for reviewing the quality stats on the read files.

Tool Source for App   

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

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