Copy-number variations (CNVs) are a type of structural variation resulting from the cell having an abnormal number of copies of one or more sections of DNA. To use QSeq for Copy Number Variation (CNV) analysis, choose File > Import Experiments > CNV, and then select your CNV files to import during the Add Experiments to Import step of the Project Setup Wizard. (For a list of supported file formats, see Supported File Types.) Target sequences, also called templates, are defined by you during the Set Up Preprocessing step of the Project Setup Wizard. Target sequences may consist of a group of contigs or a certain group of features within a genomic template.
During processing, QSeq maps reads to the set of target sequences. QSeq uses mers, defined by a sliding window of a specified number of bases (default is 15) to determine where reads are mapped to the template. Several options are available for determining the minimum requirements necessary for a read to be considered as a match to a template. You may adjust this parameter, and others, in the QSeq Advanced Options dialog. Once the reads have been processed and assigned to target sequences, signal values are created based upon the number of reads mapped to each location on the template. This count is divided by the length of the feature, or target, and then multiplied by the average target length for the entire set. By default, ArrayStar uses the log2 of these values for all visualizations and calculations.
Note: QSeq uses temporary files during the process of generating and matching mers from individual reads to the template sequences. These temporary files are stored in the directory specified under Edit > Preferences. Since processing can require a significant amount of disk space, it may be helpful to use an external hard drive for very large projects and edit the temporary directory listed under Edit > Preferences to point to the external hard drive location.