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1.  What is the definition of "Quality" for a ChIP-seq dataset?
The term "Quality" for ChIP-seq and enrichment-related datasets makes reference to the capacity of the assay of representing the enrichment events under study in the most comprehensive manner. Ideally, the best ChIP-seq dataset may cover all enrichment events related to the target molecule of interest (for the studied conditions); whereas with the decrease in quality, only the most abundant events might remained represented in the reconstructed profile.

2.  Why do I need to be concerned by the quality associated to my ChIP-seq dataset?
Currently, most of the performed ChIP-seq studies aim at comparing multiple assessed enrichment profiles with the aim of describing co-occurring events; or, low quality datasets may give rise to erroneous conclusions concerning the absence or presence of given factors. Thus, assessing the quality of the compared ChIP-seq datasets prior their comparison may help to identify potential samples presenting low quality descriptors.

3. Can I use the stand-alone version of NGS-QC for my analysis?
Though we provide the downloadable stand-alone version of NGS-QC, we strongly advice you to use the Galaxy version. Because Galaxy version contains added features which is not available in stand-alone version.