Biomedical Engineering Reference
In-Depth Information
x
[refseq_id] is the name of the assembly created by phredPhrap. The [refseq_id] is the extension
of the reference sequence trace if different from the sudophred default (.REF).
y
To learn about how to interpret Polyphred output, see the Polyphred documentation at
http://droog.gs.washington.edu/polyphred/poly_doclist.html.
PROTOCOL 2.7 Graphical Variant Discovery
with the NovoSNP program
Equipment and reagents
The
novoSNP
program
z
,
aa
•
Reference sequence(s) in FASTA format
•
Sequence trace files in binary (ABI or SCF) format.
•
Method
1 Create a new project in novoSNP. Under the File menu, select 'New Project.' In the
pop-up window, navigate to where the project will be stored and give it a name; for
example, MyNovoSNP.proj.
2 Add a reference sequence to the project. Under the Data menu, select 'Add refseq.' In
the pop-up window, navigate to the folder that contains the reference sequence and
select the FASTA file.
3 Add sequence traces to the project. Under the Data menu, select 'Add Runs.' Navigate
to the folder that contains the binary trace files, and click the 'Select' button. In the
pop-up window that appears, select the following options:
(a) Simple base qualities: Always
(b) Quality clipping: On
(c) Cutoff: 0.02.
4 Click on 'Add all' or 'Add selected' to add traces.
bb
5 View the read alignments. Under the Window menu, select 'Alignment.'
cc
6 Manually review the variants. The variants detected by novoSNP appear in a panel on
the left-hand side of the program. Click a variant to display the traces across that
position in the right-hand window. Left-clicking and dragging on the trace window will
scroll the trace display right or left. If desired, edit the settings in the novoSNP
toolbar to adjust the trace display.
7 Automatically filter the variants. Under the Window menu, select 'Filter.'
dd
8 Generate SNP or trace reports.
ee
Under the Analysis menu, select 'Reports.' Choose the
type of report required and name it.
