Opening a Sequence file

To open one or more Sequence files interactively simply run the program and select File > Open. You can then select the files you want to analyse.

Newly opened files will immediately appear in the set of tabs at the top of the screen. Because of the size of these files it can take a couple of minutes to open them. FastQC operates a queueing system where only one file is opened at a time, and new files will wait until existing files have been processed.

FastQC supports files in the following formats

* Casava fastq format is the same as regular fastq except that the data is usually split across multiple files for a single sample. In this mode the program will merge the files in a sample group and present a single report for each sample. Also Casava fastq files contain poor quality sequences which have been flagged to be remove. In Casava mode the program will exclude these flagged sequences from the report.

By default FastQC will try to guess the file format from the name of the input file. Anything ending in .sam or .bam will be opened as a SAM/BAM file (using all sequences, mapped and unmapped) , and everything else will be treated as FastQ format. If you want to override this detection and specify the file format manually then you can use the drop down file filter in the file chooser to select the type of file you're going to load. You need to use the drop down selector to make the program use the Mapped BAM or Casava file modes as these won't be selected automatically.