FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high througput sequencing pipelines. It provides a molecular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
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If you haven't used the workflow samples in UGENE before, look at the "How to Use Sample Workflows" section of the documentation. |
Workflow Sample Location
The workflow sample "Quality Control by FastQC" can be found in the "NGS" section of the Workflow Designer samples.
Workflow Image
The workflow is the following:
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<center> <br> <img src="/wiki/download/attachments/15138834/Quality Control by FastQC.png"/> <br> </center> |
Workflow Wizard
The wizard has 1 page.
High Throughput Sequence QC Report by FastQC: On this page you must input FASTQ file(s) and optionally modify advanced parameters.
HTML <center> <br> <img src="/wiki/download/attachments/16122729/Quality Control by FastQC_1.png"/> <br> </center>
The following parameters are available:
FASTQ URL(s) Semicolon-separated list of pathes to the input files. Output directory Select an output directory. Custom - specify the output directory in the 'Custom directory' parameter. Workflow - internal workflow directory. Input file - the directory of the input file. Custom directory Select the custom output directory. List of adapters
Specifies a non-default file which contains the list of adapter sequences which will be explicity searched against the library. The file must contain sets of named adapters in the form name[tab]sequence. Lines prefixed with a hash will be ignored. List of contaminants
Specifies a non-default file which contains the list of contaminants to screen overrepresented sequences against. The file must contain sets of named contaminants in the form name[tab]sequence. Lines prefixed with a hash will be ignored.