Biomedical Engineering Reference
In-Depth Information
•
Poor sample quality
: Degraded, contaminated or variable-concentration DNA samples
amplify poorly. Samples whose quality and concentration are unknown should be quan-
tified by Picogreen assay [24] and assessed for integrity by agarose gel electrophoresis
prior to PCR.
2.3.3 Working with binary trace files
Often
Phred
and other programs have difficulty reading binary files from non-native oper-
ating systems (such as MacOS). In UNIX/Linux systems, the file type of a binary sequence
trace file can be displayed using the command:
file trace.b1.ab1
where trace.b1.ab1 is the name of a trace file. The file type should be 'data.' If it is
'compressed data,' then the files can be uncompressed with the
gunzip
command. If another
file type is detected, then the trace is likely corrupt (or empty) and should be either removed
or replaced from the original file location.
2.3.4
Phred
/
Phrap
Many issues with
Phred
, especially those related to parameters, can be addressed by viewing
the usage information:
phred -doc
Alternatively, complete documentation for
Phred
is available at http://www.phrap.org/
phredphrap/phred.html.
References
1. Sherry, S.T., Ward, M.H., Kholodov, M.
et al
. (2001) dbSNP: the NCBI database of genetic
variation.
Nucleic Acids Research
,
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(1), 308 - 311.
2. Koboldt, D.C., Miller, R.D. and Kwok, P.Y. (2006) Distribution of human SNPs and its effect
on high-throughput genotyping.
Human Mutation
,
27
(3), 249 - 225.
3. Miller, R.D., Taillon-Miller, P. and Kwok, P.Y. (2001) Regions of low single-nucleotide polymor-
phism incidence in human and orangutan xq: deserts and recent coalescences.
Genomics
,
71
(1),
78 - 88.
4. The International HapMap Consortium (2005) A haplotype map of the human genome.
Nature
,
437
(7063), 1299 -1320.
5. The International HapMap Consortium (2007) A second generation human haplotype map of over
3.1 million SNPs.
Nature
,
449
(7164), 851 - 861.
6. The Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000
cases of seven common diseases and 3,000 shared controls.
Nature
,
447
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