Project Setup in the AVA Software

2.2	Project Setup in the AVA Software

2.2.1 Launching the AVA Application

2.2.2 Creating a New Project

2.2.3 Defining the Reference Sequence

2.2.4 Defining the Amplicons

2.2.5 Defining the Sample

2.2.6 Defining the Known Variant

2.2.7 Importing the Read Data Set

For our EGFR experiment example, let’s posit that a 4-region sequencing Run generated four SFF files, one of which, named “DGVS90J03.sff”, contains all the reads of our combined 11 Amplicon libraries and is now available on the local file-system.

Also, while each exon could be used individually as Reference Sequences in the Variant analysis, we decide that it would be more convenient to report on all the Variants found in all five exons together. To simplify the analysis, therefore, we create an “artificial” Reference Sequence by concatenating the sequences of the 5 exons, with strings of 20 ‘N’ characters to separate them. The resulting single Reference Sequence is shown in Table 2‑2.

Table 2‑2: “Artificial” Reference Sequence comprising exons 18 through 22 of EGFR, concatenated and with separating strings of 20 N characters

Many of the operations described through the end of section 2.4 can be done in more than one way. For example, most actions that can be performed by clicking a button can also be accessed via a contextual menu and/or by double-clicking in a field in a Table. Only one way is given in the example below; for more information, see the detailed description of each tab.