Bioinformatics for Wet-lab Scientists: Practical Application in Sequencing Analysis

Abstract

Background Genomics data is available to the scientific community after publication of research projects and can be investigated for a multitude of research questions. However, in many cases deposited data is only assessed and used for the initial publication, resulting in valuable resources not being exploited to their full depth. Main A likely reason for this is that many wetlab-based researchers do not apply bioinformatic tools themselves and therefore lack the necessary expertise. In this article, we present a series of freely available, predominantly web-based platforms and bioinformatic tools that can be combined in analysis pipelines to interrogate different types of next-generation sequencing data. Additionally to the presented exemplary route, we also list a number of alternative tools that can be combined in a mix-and-match fashion. We place special emphasis on tools that can be followed and used correctly without extensive prior knowledge in programming. Such analysis pipelines can be applied to existing data downloaded from the public domain or be compared to the results of own experiments. Conclusion Integrating transcription factor binding to chromatin (ChIP-seq) with transcriptional output (RNA-seq) and chromatin accessibility (ATAC-seq), can assist to form a deeper understanding of the molecular interactions underlying transcriptional regulation and will help establishing new hypotheses and pre-testing them in silico.