## Utilities / Define NGS experiment

### Description

The tool takes a set of count files, merges them into a single data table and associates a phenodata file so that experiment setup can be defined and downstream analyses performed.

### Parameters

- Type of experiment (ChIP-seq, RNA-seq, miRNA-seq) [RNA-seq]
- Does your data contain genomic coordinates (yes, no) [yes]
- Impute missing data (0-1000000) [0]

### Details

Takes a set of individual files with counts data and merges them into a single data table to which a phenodata file is associated. The 'group' column of the phenodata file should be edited by the user as to include information on which input files belong to a certain experiment condition. In addition, the initial - that is, before any filtering steps - library size (in bases) may be added in the 'library_size' column. If added, this information will be used for normalization purposes in downstream tools for differential expression analysis.

The tool has two modes of operation, dpendning on whether alignment has been performed using something else than a reference genome or not. For reference genome alignments, information about genomic location including chromosome, start and end coordinate will be added to the data file.

Since zero counts in data may cause issues for certain downstream applications that transform data or calculate ratios, the tool also offers the possibility to impute a fixed value to replace the zeros with. By default, the zeros are left untouched, relying on the downstream applications to handle the issue instead.

### Output

A data table with count columns and a corresponding phenodata table.