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FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular 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.
The main functions of FastQC are
- Import of data from BAM, SAM or FastQ files (any variant)
- Providing a quick overview to tell you in which areas there may be problems
- Summary graphs and tables to quickly assess your data
- Export of results to an HTML based permanent report
- Offline operation to allow automated generation of reports without running the interactive application
NOTE: FastQC will determine the format that your FASTQ reads are in (PHRED33, Illumina, etc). The detected read type will be listed on the graphs outputted. As an additional note, PHRED33 is exactly the same as Solexa / Illumina 1.9, thus if using these FASTQ files in downstream apps such as the FASTX toolkit, you will need to select PHRED33 for your format type if your reads are in Solexa/Illumina 1.9 format.
Community Data > iplantcollaborative > example_data > fastqc
Use SRR070572_hy5.fastq as test data.
All outputs can be found in the directory Community Data > iplantcollaborative > example_data > fastqc
- Expect the following as outputs (in addition to the logs generated for all analyses)
- Directory with name of the input file used
- zipped instance of this directory
- Within the directory generated (in the case of the above example, it should read SRR070572_hy5_fastqc), there are two sub directories and several files.
- Sub directories are icons (not scientifically necessary) and images.
- Files generated in this directory are the following: fastqc_data.txt, fastqc_report.html and summary.txt
- Within the image directory, the following files should be available: