macs3_bdgdiff1

Model-based analysis for chip-sequencing

Overview

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)

--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: log10LR cutoff. Regions with signals lower than cutoff will not be considerred as enriched regions. DEFAULT: 3 (likelihood ratio=1000)

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

-g, --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: 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: 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: 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.