Read Analysis

These Read Analysis tools are mostly tools that work with the [CDT or other tab-delimited Matrix file formats][file-format].

Most commonly used is the TagPileup tool.

Others manipulate files to calculate normalization factors, normalize the data, or other manipulations and transformations of read info.

Tool Name	Input	Output	Description
tag-pileup	BED + BAM	CDT	Pileup 5' ends of aligned tags given BED and BAM files according to user-defined parameters.
scaling-factor	BAM	TXT	Calculate the factor as either total tag normalization or normalization of ChIP-seq data with control. (PMID:22883957)
scale-matrix	[CDT|TAB]	TAB[..]	Apply a user-specified scaling factor to tab-delimited matrix data.
aggregate-data	[CDT|TAB][..]	TAB[..]	The AggregateData tool is used to process a bunch of matrix files into one matrix file.
transpose-matrix	[CDT|TAB]	[CDT|TAB]	Interchange the rows and columns of a matrix