Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis

Abstract

BackgroundThere has been an enormous expansion of use of chromatin immunoprecipitation followed by sequencing (ChIP-seq) technologies. Analysis of large-scale ChIP-seq datasets involves a complex series of steps and production of several specialized graphical outputs. A number of systems have emphasized custom development of ChIP-seq pipelines. These systems are primarily based on custom programming of a single, complex pipeline or supply libraries of modules and do not produce the full range of outputs commonly produced for ChIP-seq datasets. It is desirable to have more comprehensive pipelines, in particular ones addressing common metadata tasks, such as pathway analysis, and pipelines producing standard complex graphical outputs. It is advantageous if these are highly modular systems, available as both turnkey pipelines and individual modules, that are easily comprehensible, modifiable and extensible to allow rapid alteration in response to new analysis developments in this growing area. Furthermore, it is advantageous if these pipelines allow data provenance tracking.ResultsWe present a set of 20 ChIP-seq analysis software modules implemented in the Kepler workflow system; most (18/20) were also implemented as standalone, fully functional R scripts. The set consists of four full turnkey pipelines and 16 component modules. The turnkey pipelines in Kepler allow data provenance tracking. Implementation emphasized use of common R packages and widely-used external tools (e.g., MACS for peak finding), along with custom programming. This software presents comprehensive solutions and easily repurposed code blocks for ChIP-seq analysis and pipeline creation. Tasks include mapping raw reads, peakfinding via MACS, summary statistics, peak location statistics, summary plots centered on the transcription start site (TSS), gene ontology, pathway analysis, and de novo motif finding, among others.ConclusionsThese pipelines range from those performing a single task to those performing full analyses of ChIP-seq data. The pipelines are supplied as both Kepler workflows, which allow data provenance tracking, and, in the majority of cases, as standalone R scripts. These pipelines are designed for ease of modification and repurposing.

NGseqBasic - a single-command UNIX tool for ATAC-seq, DNaseI-seq, Cut-and-Run, and ChIP-seq data mapping, high-resolution visualisation, and quality control

“…However, they do not collect the data to a single-click loadable visualisation, including all the metrics and analysis reports (for tool comparisons, see Supplementary Table 1) and therefore are more time consuming and require higher levels of computational expertise of the user. Other solutions provide GUI-based analysis, where modifying the source code is more time consuming [9][10][11] . Promising database-based all-inclusive data analysis platforms have been developed 12,13 , but these are feasible for only large core facilities, where the time and effort necessary for system administration and database management becomes cost-effective.…”

RACS: Rapid Analysis of ChIP-Seq data for contig based genomes

“…The T.thermophila's genome [18] is contig based and contains almost 27 thousand annotated genes or genic regions [35]. To further the understanding of Ibd1, and to contribute to current understanding of how chromatin remodeling works, we analysed its localization within the genome by ChIP-Seq (Figure 1) [36,37,38,39]. This allowed us to understand what genes are being regulated by Ibd1.…”

CSA: a web service for the complete process of ChIP-Seq analysis

“…In addition, CSA provides the visualization of the entire process. Table 1 shows a comprehensive comparison between CSA and several other typical platforms for ChIP-seq analysis including HOMER [30], ChIPSeqWorkflow [35], ChIPseeker [31], CisGenome [36], ChIP-seq tool [37], Nebula [32], and ChIPseek [33]. Table 1 also lists the systems on which the platforms rely, the installation requirement, the interface, and the functions.…”