MultiRepMacsChIPSeq - report_mappable_space

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report_mappable_space.pl

A script to report the mappable space of a genome based on empirical mapping derived from one or more bam files. For a given ChIPSeq experiment, provide all available Bam files.

Two numbers are reported: all mappable space reported by all alignments, regardless of mapping quality and number of hits to the genome, and unique mappability, as determined by a minimum mapping quality score (default 10). Results are written to standard out.

USAGE:

report_mappable_space.pl *.bam
report_mappable_space.pl --chrskip '^chrRandom.+|chrM' *.bam

OPTIONS:

  --in <file>         An input bam file, must be sorted and indexed
                        Repeat for each input file
  --qual <int>        Minimum mapping quality to be considered unique (10)
  --chrskip <regex>   Provide a regular expression for skipping unwanted chromosomes
  --cpu <int>         Specify the number of threads to use (4)