Organising the Data
This wizard is used to build the file hierarchy that describes the original wet lab experiment similar to the image shown below.
Users should first setup their samples in Step 1. By either giving the new sample a name by entering it into the indicated box and pressing the add sample button, alternatively if this field is left blank a name will be automatically generated.
Next users must move to Step 2 configure the references to be used. This will include a mandatory genome
The sequence alignment can be either handled with PatMan  or Bowtie . If Bowtie is required users must supply the first filename in a set of pre-indexed genome files (genome pre-indexes can be found on the Bowtie website)
Following this, users can either choose to finish setup here, or supply an additional GFF file that will be used to annotate the sequences found in the sample files.
After a GFF file is specified users should move to Step 3 and select the annotations they wish to include in their result sets (The more annotations selected, the more work the software must do.)
Users can drag each annotation into either the ‘selected’ list or the ‘other’ list. Any annotations in the ‘selected’ list will be treated individually, those in the ‘other’ list will be grouped together and referred to as ‘other’ in any further analysis
 K. Prufer, U. Stenzel, M. Dannemann, R. E. Green, M. Lachmann, and J. Kelso, “PatMaN: rapid alignment of short sequences to large databases.,” Bioinformatics, vol. 24, no. 13, pp. 1530–1531, Jul. 2008.  B. Langmead, C. Trapnell, M. Pop, and S. L. Salzberg, “Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.,” Genome Biol., vol. 10, no. 3, p. R25, Jan. 2009.