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Qplot will generate ''qa.R'' which is R code used for plotting the figures in ''qa.pdf'' file. If Rscript is not installed in the system, you can use the qa.R to generate the figures in other machines, or extract plotting data from each run and combine multiple runs together to generate more comprehensive plots (See [[Example]]).
Qplot will generate ''qa.R'' which is R code used for plotting the figures in ''qa.pdf'' file. If Rscript is not installed in the system, you can use the qa.R to generate the figures in other machines, or extract plotting data from each run and combine multiple runs together to generate more comprehensive plots (See [[Example]]).
= Example =
Qplot can generate diagnostic graphs, related R code and summary statistics for each sam/bam files.
Qplot can generate diagnostic graphs, related R code and summary statistics for each sam/bam files.
== Build-in example ==
In pre-compiled binary file, you will find a subdirectory named examples. We provide a sample file from 1000 Genome project, it contained aligned read on chromosome 20 from position 8 Mbp to 9Mbp. You can use qplot using the following commandline:
In pre-compiled binary file, you will find a subdirectory named examples. We provide a sample file from 1000 Genome project, it contained aligned read on chromosome 20 from position 8 Mbp to 9Mbp. You can use qplot using the following commandline:
== Gallery of examples ==
Here we show qplot can be applied in different sequencing scenarios. Also users can customize statistics generated by qplot in various formats.
Here we show qplot can be applied in different sequencing scenarios. Also users can customize statistics generated by qplot in various formats.
== Diagnose sequencing quality ==
Qplot is designed and implemented by the need of checking 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,
Besides the exampled of analyzing RNA-seq data as in the manuscript,
