What is it?
BaseSpace converts *.bcl files into FASTQ files, which contain base call and quality information for all reads passing filtering.
When to use it.
FASTQ files can be used as sequence input for alignment and other secondary analysis software.
When not to use it.
Do not use it with tools that are not compatible with the FASTQ format.
How to use it
BaseSpace automatically generates FASTQ files in sample sheet-driven workflow apps. Other apps that perform alignment and variant calling also automatically use FASTQ files.
FASTQ files are saved compressed in the GNU zip format (an open source file compression program), indicated by the .gz file extension.
Each entry in a FASTQ file consists of four lines:
For the Undetermined FASTQ files only, the sequence observed in the index read is written to the FASTQ header in place of the sample number. This information can be useful for troubleshooting demultiplexing.
@<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<x-pos>:<y-pos> <read>:<is filtered>:<control number>:<sample number>
The following table describes the elements:
An example of a valid entry is as follows; note the space preceding the read number element:
If the read is not identified as a control, then the 10th column (<control number>) is zero. If the read is identified as a control, the number is greater than zero, and the value specifies what type of control it is. The value is the decimal representation of a bit-wise encoding scheme. In that scheme bit 0 has a decimal value of 1, bit 1 a value of 2, bit 2 a value of 4, and so on.
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