Contents
What does a FASTQ file contain?
A FASTQ file is a text file that contains the sequence data from the clusters that pass filter on a flow cell (for more information on clusters passing filter, see the “additional information” section of this bulletin). If samples were multiplexed, the first step in FASTQ file generation is demultiplexing.
What are paired end Fastq files?
Paired end reads are usually provided as two fastq-format files, with each file representing one end of the read. Fastq-format files have become the dominant file format for sharing DNA sequences as they conveniently contain both the sequence and quality information in a single file (1).
Can a FASTQ file have two FASTQ files?
If a sample has two fastq files it is likely that the reads are paired end. It is to note however that with a single file it is not possible to exclude that paired end reads can be interleaved in one single file, even if it is not common (in my opinion);
What to do with FASTQ data from exome?
If you received a FASTQ file from an exome or whole genome sequencing test, our guide for using genome sequencing data files is a great place to start. It provides insight into what type of data each of the sequencing files contains and which files are the best to use with DNA analysis apps and reports.
What does a FASTQ file look like in Illumina?
For a paired-end run, one R1 and one Read 2 (R2) FASTQ file is created for each sample for each lane. FASTQ files are compressed and created with the extension *.fastq.gz. What does a FASTQ file look like?
How big is a FASTQ file in R1?
Here is an example of a single entry in a R1 FASTQ file: More detailed information on the FASTQ sequence file format can be found here. FASTQ files can contain up to millions of entries and can be several megabytes or gigabytes in size, which often makes them too large to open in a normal text editor.