Elementolab/ChIPseeqerPlotAverageReadDensityInGenes

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ChIPseeqerPlotAverageReadDensityInGenes

To run the tools directly from any folder, you need to add the $CHIPSEEQERDIR and $CHIPSEEQERDIR/SCRIPTS to your $PATH variable. Read How to set the CHIPSEEQERDIR variable.

This program takes as input a list of genes and a directory containing read files (1 per chromosome), and will draw an average read density profile for these genes only.

Arguments include the directory where the aligned reads are located (--chipdir=DIR) and a gene list (--genelist=FILE, or --genelist=all means that all genes will be used).

There are two modes: the first mode shows average normalized read densities for upstream regions, exon 1, intron 1, all exons, all introns, and downstream regions. To use this mode, specify --geneparts=all and --q=INT. --q specifies the bin size (eg 250 for 250bp).

ChIPseeqerPlotAverageReadDensityInGenes --genelist=all --chipdir=CHIP --geneparts=all --q=250

The second mode shows read densities for upstream regions, gene bodies, and downstream regions only. This mode requires --geneparts=body and specifying --numbins=INT (number of bins per gene part).

ChIPseeqerPlotAverageReadDensityInGenes --genelist=all --chipdir=CHIP --geneparts=body --numbins=20

The following options are available:

--chipdir=DIR     directory with reads
--geneparts=STR   what type of plot: all or body
--q=INT           bin size (bp)
--numbins=INT     number of bins (for geneparts=body)
--format=STR      eland, sam, etc
--genome=STR      can be hg18 (human),
                  mm9 (mouse),
                  dm3 (drosophila), or
                  sacser (for Saccharomyces cerevisiae)
--db=STR          can be refSeq (available for hg18, mm9, dm3), 
                  AceView (for hg18, mm9), 
                  Ensembl (for hg18, mm9, dm3)
                  UCSCGenes (for hg18, mm9). 
                  Default is refSeq.
--h=INT           plot height in pixels (default 300)
--ymax=FLOAT      ylim (0.5 by default)
--suffix=STR      by default, the output file (PDF) is called genelist.genedataprofiles.plot.pdf. 
                  Using this option creates    genelist.genedataprofiles.plot.STR.pdf
--getprofiles=INT set to 0 if you only want to change graphical display parameters
--normalize=STR   two modes: max or rpkm (usually produce similar results; default is max)
--useprofiles=FILE advanced use. Use this option to specify a precalculated 
                   database of profiles instead of getting new ones. 
                   This database is automatically generated when using --genelist=all (and not --useprofiles)

Here's an example of plot created using this program (--geneparts=all --q=250, it look much nicer as PDF) :

Here's another example (--geneparts=body --numbins=20) :