This application writes out of file that is compatible with both TSV (tab separated values) and GNUPlot, a command line plotting tool available on Linux, Mac OSX and Windows.

Running the Program

The program runs as follows:

 $ plot_qscore_histogram 140131_1287_0851_A01n401drr

In this sample, 140131_1287_0851_A01n401drr is a run folder and the summary is written to the standard output.

 # Version: v1.0.4-117-g05ea745-dirty
 # Run Folder: 1Read0Index_120423_117213Bin1R0I
 set terminal png nocrop
 set output 'q-hist.png'
 set style fill solid noborder
 set title "D0TM0ACXX All Lanes"
 set style data histograms
 set yrange [0 : 2.148 ]
 set xrange [1 : 38.5 ]
 set ylabel "Total (million)"
 set xlabel "Q Score"
 plot "-" using 1:2:3:xtic(1) with boxes notitle
 0       0       0
 10      0.0119  10
 20      0.003569        5
 25      0.036075        5
 30      1.95263 5
 0       0       0
 0       0       0

Available Options

The following options are supported in addition to the run folder. They must be given in the form: --filter-by-lane=1 with no additional space between the option name and value.

Filter Options

--filter-by-lane=<lane number>: Only the data for the selected lane will be displayed
--filter-by-channel=<channel number>: Only the data for the selected channel will be displayed
--filter-by-base=<(A,C,G,T)>: Only the data for the selected base will be displayed
--filter-by-surface=<surface number>: Only the data for the selected surface will be displayed
--filter-by-read=<read number>: Only the data for the selected read will be displayed
--filter-by-cycle=<cycle number>: Only the data for the selected cycle will be displayed
--filter-by-lane=<lane number>: Only the data for the selected lane will be displayed
--filter-by-tile-number=<tile number>: Only the data for the selected tile number will be displayed
--filter-by-swath=<swath number>: Only the data for the selected swath will be displayed
--filter-by-section=<section number>: Only the data for the selected section will be displayed