Scaling Factor

Calculate a normalization factor using the total tag method or normalization of ChIP-seq data with control (NCIS) method by Liang & Keles (BMC Bioinf 2012).

File input (BAM)

The scaling factors are calculated directly from a BAM file and are calculated on a per-BAM basis. The scaling factor determined for one file should not be used to normalize data from another BAM file.

caution

Make sure your BAM input files are sorted and indexed.

Scaling Methods

• Total Tag normalization
• NCIS normalization
• Both total tag and NCIS methodologies

Command Line Interface

Usage:

java -jar ScriptManager.jar read-analysis scaling-factor [-t | -n | -b] [-hV]
[-c=<controlBAM>] [-f=<blacklistFilter>] [-m=<minFrac>]
[-o=<outputBasename>] [-w=<window>] <bamFile>

Option	Description
-f, --blacklist=<blacklistFilter>	specify blacklist file to filter by
-c, --control=<controlBAM>	control BAM file (to use with -n or -b flags)
-w, --window-size=<window>	window size for NCIS-related scaling types (default=500)
-m, --min-fraction=<minFrac>	minimum fraction for NCIS-related scaling types (default=0.75)

Positional Input

This tool takes a single BAM file for input. As with other tools, this tool requires the BAM file be indexed.

Output Options

Option	Description
-o, --output=<outputBasename>	specify output file for composite values

Scale Options

Option	Description
-t, --total-tag	total tag scaling (default)
-n, --ncis	ncis normalization with window size in bp and unitless minimum fraction (default-size=500, default-fraction=0.75)
-b, --both	ncis with total tag (default-size=500, default-fraction=0.75)

Liang & Keles (BMC Bioinf 2012)