Integrated Bioinformatics Workflow for NGS Data

Pipelines for primary analysis (filtering and alignment to the reference genome of the raw reads) and secondary analysis (expression quantification, differential gene expression and peak calling) have been integrated in the HTS-flow system^{89 (link)}. Bioinformatic and statistical analysis were performed using R with Bioconductor packages and comEpiTools packages^{90 ,91} . Motif analysis was performed using CentriMo software^{92 (link)}. Intron analysis was performed with the INSPEcT tool^{93 (link),94 (link)}. Gene lists from RNA and ChIP sequencing were analysed in Enrichr⁹⁵ . Statistical analyses for IHC and qRT-PCR were performed using GraphPad Prism v6.0d (GraphPad Software, Inc., San Diego, CA, USA) as indicated with P ≤ 0.05 considered to be statistically significant. Venn diagrams were draw in the interactive tool Venny [https://bioinfogp.cnb.csic.es/tools/venny/index.html].