NAME

       macs2_bdgdiff - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

       usage: macs2 bdgdiff [-h] --t1 T1BDG --t2 T2BDG --c1 C1BDG --c2 C2BDG

       [-C CUTOFF] [-l MINLEN] [-g MAXGAP] [--d1 DEPTH1]
              [--d2 DEPTH2] [--outdir OUTDIR] (--o-prefix OPREFIX | -o OFILE OFILE OFILE)

   optional arguments:
       -h, --help
              show this help message and exit

       --t1 T1BDG
              MACS  pileup  bedGraph  for  condition 1. Incompatible with callpeak --SPMR output.
              REQUIRED

       --t2 T2BDG
              MACS pileup bedGraph for condition 2. Incompatible  with  callpeak  --SPMR  output.
              REQUIRED

       --c1 C1BDG
              MACS  control  lambda  bedGraph for condition 1.  Incompatible with callpeak --SPMR
              output. REQUIRED

       --c2 C2BDG
              MACS control lambda bedGraph for condition 2.  Incompatible  with  callpeak  --SPMR
              output. REQUIRED

       -C CUTOFF, --cutoff CUTOFF
              logLR cutoff. DEFAULT: 3 (likelihood ratio=1000)

       -l MINLEN, --min-len MINLEN
              Minimum  length  of  differential region. Try bigger value to remove small regions.
              DEFAULT: 200

       -g MAXGAP, --max-gap MAXGAP
              Maximum gap to merge nearby differential regions.  Consider a wider gap  for  broad
              marks. Maximum gap should be smaller than minimum length (-g). DEFAULT: 100

       --d1 DEPTH1, --depth1 DEPTH1
              Sequencing  depth (# of non-redundant reads in million) for condition 1. It will be
              used together with --d2.  See description for --d2 below for how  to  assign  them.
              Default: 1

       --d2 DEPTH2, --depth2 DEPTH2
              Sequencing  depth (# of non-redundant reads in million) for condition 2. It will be
              used together with --d1.  DEPTH1 and DEPTH2  will  be  used  to  calculate  scaling
              factor  for  each  sample, to down-scale larger sample to the level of smaller one.
              For example, while comparing 10 million condition 1 and 20 million condition 2, use
              --d1  10  --d2 20, then pileup value in bedGraph for condition 2 will be divided by
              2. Default: 1

       --outdir OUTDIR
              If specified all output files will be  written  to  that  directory.  Default:  the
              current working directory

       --o-prefix OPREFIX
              Output   file   prefix.   Actual   files   will   be   named  as  PREFIX_cond1.bed,
              PREFIX_cond2.bed and PREFIX_common.bed. Mutually exclusive with -o/--ofile.

       -o OFILE OFILE OFILE, --ofile OFILE OFILE OFILE
              Output filenames. Must give three arguments in order: 1. file for unique regions in
              condition  1; 2. file for unique regions in condition 2; 3. file for common regions
              in both conditions. Note: mutually exclusive with --o-prefix.