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.