If you are following a CNV or RNA-Seq workflow, the Set Up Preprocessing step of the Project Setup Wizard allows you to select the normalization method and specify the template sequence(s).
Choose from the following preprocessing options for CNV and RNA-Seq data:
•Preprocessing Method – This has an unchangeable default of QSeq.
•Normalization method – Choose the desired normalization method to be applied to your data. The methods available vary depending on the type of data you are importing. A brief description of the selected method will appear underneath the selection. For the CNV workflow, normalization is on a per exon basis, and options are None, RPKM-CN or zRPKM. For the RNA-Seq workflow, normalization is on a per isoform basis, and options are None, RPM, RPKM, RPK, DESeq2, DESeq2-Local, edgeR and edgeR-Local.
•If enabled, use Find File or Find All to load the template sequences that your reads will be mapped to. Templates may be a single sequence, or group of sequences, such as a set of contigs. Use Download to launch the Download Genome Reference dialog and download your template sequences directly from NCBI. If desired, use the Remove button to clear the selected sequence, or the Remove All button to clear all of the template files and begin again.
•Use sequences as genes – Each entire template sequence is used as a target for mapping reads. The total number of template sequences you have loaded, as well as total length of the sequences, are noted to the right of this option. In RNA-Seq workflows, the sequences are treated as isoforms rather than genes.
•Use features of type(s) – Only features of the type you specify will be used as targets for mapping reads. You may select a feature type from the dropdown list provided, or you may enter multiple feature types in this field by typing them in and separating each with a comma. The list of feature types in the dropdown list will reflect the feature types contained within the template sequences you have loaded. If your template sequences do not contain features, this option will be inactive. The total number and length of features, based upon the type you have specified, are listed to the right of this option and will update as the selection changes.
•Configure Advanced Options – Click this button if you would like to further adjust the processing parameters or to export a graph, alignment, or file of unassigned reads.
Click Back to return to the Add Experiments to Import step of the Project Setup Wizard; Next to process your data and proceed to the next step of the wizard; or Cancel to close the Project Setup Wizard without adding any data to the project.