Following a MatrixREDUCE (http://reducesuite.bussemakerlab.org/documentation/matrixreduce/) or MotifREDUCE (http://reducesuite.bussemakerlab.org/documentation/motifreduce/) run, a bunch of output files (model parameters, PSAMs etc.) are generated. The HTMLSummary utility program is provided to summarize the main results in a intuitive, easy to follow HTML page so that (even non-expert) users can quickly make sense of their findings, e.g., the top list of significant PSAMs (motifs). Internally, HTMLSummary makes system-calls to the utility program LogoGenerator (http://reducesuite.bussemakerlab.org/documentation/logogenerator/) to create the logo images. These inter-connected programs, plus a few others, constitute the REDUCE Suite.
HTMLSummary [options] [-file=HTMLFile]
Required parameters:
none
Optional parameters:
[-output=dir_name] --- path to an MatrixREDUCE/MotifREDUCE run directory,
used both as input and output for HTML summary (./)
[-copy] --- copy CSS, JavsScript and associated image files to
the output directory to make the HTML self-contained
[-rc] --- logo based on reverse complementary strand
[-width=ThumbnailImageWidthInPixel] (145)
[-height=ThumbnailImageHeightInPixel] (90)
[-psam_list=list_of_PSAMs] --- generate a summary LOGO page for the list
of PSAMs in the file
[-file=HTMLFile] --- HTML output file name (index.html)
Usage: (following a MatrixREDUCE (http://reducesuite.bussemakerlab.org/documentation/matrixreduce/) run)
HTMLSummary
HTMLSummary -psam=psams.list -file=psams.html