The CLC Cancer Research Workbench supports data from Illumina's Genome Analyzer, HiSeq 2000 and the MiSeq systems. Choosing the Illumina import will open the dialog shown in figure 6.6.

Image importngsdialog-illumina
Figure 6.6: Importing data from Illumina systems.

The file formats accepted are:

Paired data in any of these formats can be imported.

Note that there is information inside qseq and fastq files specifying whether a read has passed a quality filter or not. If you check Remove failed reads these reads will be ignored during import. For qseq files there is a flag at the end of each read with values 0 (failed) or 1 (passed). In this example, the read is marked as failed and if Remove failed reads is checked, the read is removed.

For fastq files, part of the header information for the quality score has a flag where Y means failed and N means passed. In this example, the read has not passed the quality filter:
    @EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG
Note! In the Illumina pipeline 1.5-1.7, the letter B in the quality score has a special meaning. 'B' is used as a trim clipping. This means that when selecting Illumina pipeline 1.5-1.7, the reads are automatically trimmed when a B is encountered in the input file. This will happen also if you choose to discard quality scores during import.

If you import paired data and one read in a pair is removed during import, the remaining mate will be saved in a separate sequence list with single reads.

For all formats, compressed data in gzip format is also supported (.gz).

The General options to the left are:

Click Next to adjust how to handle the results. We recommend choosing Save in order to save the results directly to a folder, since you probably want to save anyway before proceeding with your analysis. There is an option to put the import data into a separate folder. This can be handy for better organizing subsequent analysis results and for batch processing.