Illumina Custom Reads
Import Illumina fastq files with support and special handling of index and more than two read files.
Most options are the same as the normal Illumina importer, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Illumina.html.
- Custom reads options. Choose how to import any combination of fastq files (like ID_S1_L002_R3_001.fastq and ID_S28_L999_I4_321.fastq) as single or paired sequence lists. This field supports 1 (for single) or 2 (for paired) values separated by comma. A value defines which fastq file or files to import, multiple fastq files means the symbols and quality scores from reads in the fastq files are concatenated in the order they are listed. A value refer to fastq files based on the read part of their names, i.e. R1, R2, R3, I1, I2, I3. The reads in the fastq files must have the same number of reads and the reads must be ordered to be consistent with each other.
For example, to import paired reads from R1, R2, R3 fastq files where R1 has forward reads, R3 has reverse reads, and R2 has molecular indices, set the custom reads options to 'R2 R1, R3'. The imported paired sequence list can now be used by tools that support symbols at the begining of read 1 of paired reads.
Non-standard fastq file names are supported when they define their type (e.g. contain "_R1", "_R2", "_I3", etc.) and, optionally, define a lane (e.g. contain "_L001", "_L002", "_L1"). The sample name for non-standard fastq files is the file name excluding the part defining read type and the part defining lane (when joining reads from different lanes).