NAME

       pscan_chip - ChIP-based identifcation of TF binding sites

SYNOPSIS

       pscan_chip -r region_file.bed -M matrixfile.wil -g genome [OPTIONS]

OPTIONS

   MANDATORY OPTIONS:
       -r  [regionfile]  the BED file with the regions to be analyzed TFs enrichment (e.g. peaks from a ChIP-Seq
       experiment). PscanChIP will compute the central position of each region and consider the  genomic  region
       surrounding  it in its computations. The default length of the region surrounding the center is 150bp but
       it can be modified using the -s option. For optimal results we suggest to use summits?? coordinates  when
       available instead of peak coordinates.

       -g  [folder]  the  genome  folder  to which the BED file refers to. The directory must contain the genome
       files in RAW format (one file per chromosome).

       -M [matrixfile] the file containing the motif matrices to be used by Pscan_ChIP.

   OTHER OPTIONS:
       -s [size] the genomic regions size, default is 150bp. Leaving the default value assures  optimal  results
       in  most  cases.  Beware  that  changing  the  region  length  makes  the  available  background  file(s)
       inconsistent, since they were computed for regions of 150 bp. Thus, to change the genomic region size  to
       be analyzed you will also need to produce new background file(s) for the new region size. All in all, for
       a normal ChIP-Seq experiment it??s better to leave this parameter untouched.

       -m [matrixname] use this option to select a matrix from matrixfile and  make  Pscan_ChIP  run  in  single
       matrix mode.

       -bg [bgfile] Background file, needed to compute global pvalues.

       -ss Single strand mode.

   OUTPUT:
       Output  files  will  be  written in a regionfile.res file, with regionfile being the name of the BED file
       passed with the -r parameter. When running in single matrix mode the  output  file  will  have  a  ".ris"
       extension instead.

       EXAMPLES:

       1- Running PscanChIP with a precomputed background file using Jaspar matrices and human genome (hg19):

       pscan_chip -r input.bed -g hg19 -M jaspar.wil -bg BG/K562.jaspar.bg

       2-  Running PscanChIP in single matrix mode to obtain the position of the best matches for a given matrix
       within the input regions (one match per region).

       pscan_chip -r input.bed -g hg19 -M jaspar.wil -m MA0493.1

       3- Preparing a new background file for a custom set of matrices or for a new set  of  accessible  genomic
       locations.

       pscan_chip -r background.bed -g hg19 -M mymatrices.wil

       The background.bed.res file obtained can be used as a background file for successive PscanChIP runs using
       the same mymatrices.wil matrices file.

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.