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= Introduction =
= Introduction =
The qplot program calculates various summary statistics some of which are plotted in a PDF file. These statistics can be used to assess the sequencing quality of sequence reads mapped to the reference genome. The main statistics are empirical Phred scores which are calculated based on the background mismatch rate. Background mismatch rate is the rate that sequenced bases are different from the reference genome, EXCLUDING dbSNP positions. Other statistics include GC biases, insert size distribution, depth distribution, genome coverage, empirical Q20 count, and so on.
The qplot program calculates various summary statistics some of which are plotted in a PDF file. These statistics can be used to assess the sequencing quality of sequence reads mapped to the reference genome. The main statistics are empirical Phred scores which are calculated based on the background mismatch rate. Background mismatch rate is the rate that sequenced bases are different from the reference genome, EXCLUDING dbSNP positions. Other statistics include GC biases, insert size distribution, depth distribution, genome coverage, empirical Q20 count, and so on.
== Binary Download ==
== Binary Download ==
We have prepared a pre-compiled (under Ubuntu) qplot along with source code . You can download it from: [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot.20120213.tar.gz qplot.20120213.tar.gz (File Size: 1.7G)]
We have prepared a pre-compiled (under Ubuntu) qplot along with source code . You can download it from: [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot.20120602.tar.gz qplot.20120602.tar.gz (File Size: 1.7G)]
The executable file is under qplot/bin/qplot.
The executable file is under qplot/bin/qplot.
== Source Code Distribution ==
== Source Code Distribution ==
We provide a source code only download in [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-source.20120213.tar.gz qplot-source.20120213.tar.gz]. Optionally, you can download example file and/or data file:
We provide a source code only download in [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-source.20120602.tar.gz qplot-source.20120602.tar.gz]. Optionally, you can download example file and/or data file:
[http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-example.tar.gz example]: example input file, and expected outputs if you following the [[#Built-in example | direction]].
[http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-example.tar.gz example]: example input file, and expected outputs if you following the [[#Built-in example | direction]].
* 1. Unarchive downloaded file
* 1. Unarchive downloaded file
tar zvxf qplot-source.20120213.tar.gz
tar zvxf qplot-source.20120602.tar.gz
A new folder ''qplot'' will be created.
A new folder ''qplot'' will be created.
== Command line ==
== Command line ==
After you obtain the qplot executable (either by compiling the source code or by downloading the pre-compiled binary file), you will find the executable file under qplot/bin/qplot.
After you obtain the qplot executable (either by compiling the source code or by downloading the pre-compiled binary file), you will find the executable file under qplot/bin/qplot.
Read group to process : --readGroup []
Read group to process : --readGroup []
Input file options : --noeof
Input file options : --noeof
Output files : --plot [], --stats [], --Rcode []
Output files : --plot [], --stats [], --Rcode [], --xml []
Plot labels : --label [], --bamLabel []
Plot labels : --label [], --bamLabel []
