NAME

       mac3_bdgdiff - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

       usage: macs3 bdgdiff [-h] --t1 T1BDG --t2 T2BDG --c1 C1BDG --c2 C2BDG

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

   options:
       -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
              log10LR  cutoff.  Regions  with  signals  lower  than  cutoff  will not be considerred as enriched
              regions. 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

       --verbose VERBOSE
              Set verbose level of runtime message. 0: only show critical message, 1:  show  additional  warning
              message, 2: show process information, 3: show debug messages.  DEFAULT:2

       --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.

macs3 bdgdiff 3.0.1                                April 2024                                    MAC3_BDGDIFF(1)