xenial (1) macs2_bdgdiff.1.gz

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.