# Which tools can I find in the deepTools Galaxy?¶

As mentioned before, each Galaxy installation can be tuned to the individual interests. Our goal is to provide a Galaxy that enables you to quality check, process and normalize and subsequently visualize your data obtained by high-throughput DNA sequencing.

Tip

If you do not know the difference between a BAM and a BED file, that’s fine. You can read up on them in our Glossary of NGS terms.

Tip

For more specific help, check our Galaxy-related FAQ and the Step-by-step protocols.

We provide the following kinds of tools:

## deepTools¶

The most important category is called “deepTools” that contains all the main tools we have developed.

### Tools for BAM and bigWig file processing¶

 multiBamSummary get read counts for the binned genome or user-specified regions multiBigwigSummary calculate score summaries for the binned genome or user-specified regions correctGCBias obtain a BAM file with reads distributed according to the genome’s GC content bamCoverage obtain the normalized read coverage of a single BAM file bamCompare normalize 2 BAM files to each other (e.g. log2ratio, difference) bigwigCompare normalize the scores of two bigWig files to each other (e.g., ratios) computeMatrix compute the values needed for heatmaps and summary plots

### Tools for QC of NGS data¶

 plotCorrelation calculate and visualize the pairwise Spearman or Pearson correlation of read counts (or other scores) plotPCA perform PCA and visualize the results plotFingerprint assess the ChIP enrichment strength bamPEFragmentSize obtain the average fragment length for paired-end samples computeGCBias assess the GC bias by calculating the expected and observed GC distribution of aligned reads plotCoverage obtain the normalized read coverage of a single BAM file

### Heatmaps and summary plots¶

 plotHeatmap visualize read counts or other scores in heatmaps with one row per genomic region plotProfile visualize read counts or other scores using average profiles (e.g., meta-gene profiles)

For each tool, you can find example usages and tips within Galaxy once you select the tool.

In addition, you may want to check our pages about Example usage, particularly Step-by-step protocols.

## Working with text files and tables¶

In addition to deepTools that were specifically developed for the handling of NGS data, we have incorporated several standard Galaxy tools that enable you to manipulate tab-separated files such as gene lists, peak lists, data matrices etc.

There are 3 main categories;

### Text manipulation¶

Unlike Excel, where you can easily interact with your text and tables via the mouse, data manipulations within Galaxy are strictly based on commands.

If you feel like you would like to do something to certain columns of a data set, go through the tools of this category!

Example actions are: * adding columns * extracting columns * pasting two files side by side * selecting random lines * etc.

A very useful tool of this category is called Trim: if you need to remove some characters from a column, this tool’s for you! (for example, sometimes you need to adjust the chromosome naming between two files from different source - using Trim, you can remove the “chr” in front of the chromosome name)

### Filter and Sort¶

In addition to the common sorting and filtering, there’s the very useful tool to select lines that match an expression. For example, using the expression c1=='chrM' will select all rows from a BED file with regions located on the mitochondrial chromosome.

### Join, Subtract, Group¶

The tools of this category are very useful if you have several data sets that you would like to work with, e.g. by comparing them.

## Basic arithmetics for tables¶

We offer some very basic mathematical operations on values stored with tables. The Summary Statistics can be used to calculate the sum, mean, standard deviation and percentiles for a set of numbers, e.g. for values stored in a specific column.

More help

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