s3v2Norm

s3v2Norm is a tool to Simultaneously normalize the Signal in peak regions and the Signal in background regions of epigenomic data sets. Detail algorithms can be viewed: https://doi.org/10.1093/nar/gkaa105

Usage: s3v2Norm [options] -o <output> -m <metadata> -n <windows_name> [-b <bin_size>]
       s3v2Norm [options] -o <output> -m <metadata> -b <bin_size> -s <species> [-n <windows_name>]
       s3v2Norm [options] -o <output> -m <metadata> -b <bin_size> -g <genomesizes> -n <windows_name> [-B <blackList>]

Content

Required arguments

-b <bin_size>

Bin size (in base pairs). [Default: 200]

-o <output>

Output directory path. [Default: ./]

-m <metadata>

Path to a metadata file (tab-delimited) for normalization, containing the Cell, Marker, ID, Exp_bigwig file, and CT_bigwig (optional) file info [Default: None]. Example:

293T H3K4me3  rep1  /PATH/TO/H3K4me3_rep1.bw   /PATH/TO/H3K4me3_rep1_CT.bw
293T H3K27ac  rep1  /PATH/TO/H3K27ac_rep1.bw
...

-s <species>

Supported species: hg38, hg19, or mm10. Selecting this option automatically loads the corresponding genomesizes file and blacklist file. If your species is not listed, manually provide these files via -g <genome_sizes> -n <windows_name> [-B <blackList>]. [Default: None]

-g <genomesizes>

Required if -s is unspecified. Path to a genomesizes file (tab-delimited) listing chromosome lengths [Default: None]. Example:

chr1  249250621
...

-n <windows_name>

Required if -s is unspecified. A unique name to identify the generated window bins for downstream processing. [Default: None]

Optional arguments

-c

Continue running a partially finished normalization process. Use this option to resume a normalization process interrupted by an error. [Default: false]

-d <id_name>

Project name [Default: chromIDEAS]. The output results will be placed into:

• ${out_dir}/${id_name}_bws_RC/: normalized signal files.

• ${out_dir}/${id_name}_bws_NBP/: used for downstream chromatin state segmentation analysis.

-B <blackList>

Path to the blacklist file (tab-delimited). If -s is set to hg38/hg19/mm10, the default blacklist is used [Default: None]. Example:

chr1  200 3000
...

-p <nthreads>

Number of parallel processes. [Default: 4]

-l <local_bg_bin>

Local background bin number. If set local_bg_bin=5, this means when the target bin is bin10, the surrounding background bins are bin5-9 and bin11-15. [Default: 5]

-h

Show this help message and exit.

-v

Show program’s version number and exit.