filter_counts - read a ChIP-seq data file and filters out all read counts

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

filter_counts 1.5.5                                March 2020                                   FILTER_COUNTS(1)

              - version 1.5.5 where options are:

       -h     Show this help text

       -d     Print debug information

       -f     Feature defining the user-defined regions of interest (default=RMSK)

       -r     Retain Mode on

              The  program reads a ChIP-seq data file (or from stdin [<]) in SGA format (<SGA File>) and filters
              out all read counts that occur within user-defined  regions  of  interest,  such  as  Repeat  Mask
              regions  (feature=RMSK).   If 'Retain Mode' is on, it only retains those lines that are within the
              user-defined regions, in which case the annotation of the user-defined regions  is  added  to  the
              output SGA file.

       filter_counts - read a ChIP-seq data file and filters out all read counts

filter_counts [options] [<] <SGAFile>