HTProcess-prepare_directories-and-run_fastqc-0.1
- de-confluence
- Roger Barthelson
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
- To use HTProcess-prepare_directories-and-run_fastqc-0.1, import your data in fastq format.
- Resources: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Test Data
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data ->Â 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 ->Â htprocess1 -> HTProcess_fastqc ->Â
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  Â