ABSTRACT
This chapter introduces quality checks that are commonly applied to all high-throughput sequencing (HTS) datasets. General quality control of the HTS reads is the first step in every Chromatin immunoprecipitation sequencing (ChIP-seq) data analysis workflow. Several programs offer an easy-to-use quality control for HTS data. Several metrics address the library preparation quality. If substantial quality drops are visible, the reads should be either trimmed or discarded. Low-quality sequences in a read may impair its genomic alignment. The HTS reads are cleaned from excess adapter sequences and low-quality bases. This can be achieved by completely removing the respective reads, thereby maintaining equal read lengths throughout the dataset, or by trimming them. Most ChIP-seq datasets with short read length will not require low-quality trimming. If necessary, the trimming parameters should be adjusted to keep the samples as comparable as possible.
