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Line 97: − + − ** This is a pdf file containing 2 pages each with 4 figures. If --pages 1 is specified, only page 1 is output. The plot is generated using Rscript. − * --stats qa.stats − ** This is a text file containing various summary statistics for each input bam/sam file − * --Rcode qa.R − ** This is the R code used for plotting the figures in qa.pdf file. If Rscript is not installed in the system the qplot is run, 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. + + + + + + + + +
→Output files
There are three (optional) output files.
There are three (optional) output files.
* --plot qa.pdf
* --plot ''qa.pdf''
Qplot will generate a PDF file named ''qa.pdf'' containing 2 pages each with 4 figures. If --pages 1 is specified, only page 1 is output. The plot is generated using Rscript.
* --stats ''qa.stats''
Qplot will generate a text file names ''qa.stats'' containing various summary statistics for each input bam/sam file.
* --Rcode ''qa.R''
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 output ==
== Example output ==
