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[http://www-personal.umich.edu/~zhanxw/qplot.Pool.9847.html QPlot of 24 samples(HTML) ]
[http://www-personal.umich.edu/~zhanxw/qplot.Pool.9847.html QPlot of 24 samples(HTML) ]
=== Diagnose sequencing quality ===
Qplot is designed and implemented by the need of checking sequencing quality.
Besides the exampled of analyzing RNA-seq data as in the manuscript,
here we demonstrate two scenarios in which qplot help us identify potential problem after obtaining sequencing data.
* Base quality distributed abnormally
[[Media: WrongBaseQual.pdf | Example of qplot help identify wrong phred base quality]]
By checking the first graph "Empirical vs reported Phred score", we found reported base qualities are shifted to right.
Further we notice that effects is caused by different software from Illumina sequencers.
In this particular example, all base qualities are wrongly added '33'. Such data used in variant calling may increase false positive SNP calling.
* Bar-coded samples
[[Media: WrongBarCoding.pdf | Example of qplot identifying the effect of ignoring bar-coding]]
By checking "Empirical phred score by cycle" (top right graph on the first page), we notice the empirical qualities in the first several cycle are abnormally low. This question leads us hypnotize the first several bases have different properties. Further investigation revealed that this sequencing was done using bar-coded DNA samples, but the analysis did not properly de-multiplexing to each sample.
== Contact ==
== Contact ==
Questions and requests should be sent to Bingshan Li ([mailto:bingshan@umich.edu bingshan@umich.edu])
Questions and requests should be sent to Bingshan Li ([mailto:bingshan@umich.edu bingshan@umich.edu])
