Fig. 1

Examples of NGS signal visualization using VING. a Strand-specific “classic” visualization of 21–25 nucleotides small RNA densities along the SPAC167.03c locus in rdp1Δ Schizosaccharomyces pombe control cells (vector) or cells overexpressing Dcr1. Signal from each library is shown in a separate panel. Reads mapped on the + and − strands are shown on the top and bottom sides of the 0 horizontal line, respectively (additional representation in different colors optional). Annotated genomic features are represented as “box” (ORF) and “line” (mRNA). Original data described in [9]. The Y axis (log₂ tag densities) shows the log₂ of the number of reads (or pairs of reads in case of paired-end sequencing) at each position. b Unstranded “line” visualization of RNA Polymerase II ChIP-seq profile along the YDL140C (RPO21) locus in a wild-type strain of Saccharomyces cerevisiae. Signal intensity for each library is represented by a different colored line (IP, black; input, green). Strands are as in the “classic” view. Annotated ORF are represented as “box”. Original data described in [10]. Y axis see above. c Strand-specific “line” visualization of the NET-seq profile along the same region as B in wild-type (black) and dst1Δ (red) cells of S. cerevisiae. Original data described in [11]. Y axis see above. d Strand-specific “heatmap” visualization of the paired-end total RNA-seq signal along the YBR019C-YBR020W (GAL10-GAL1) locus in two biological replicates of S. cerevisiae wild-type cells grown in glucose- or shifted for 1 h in galactose-containing medium. Distinct panels are used for each strand. In each panel, each lane corresponds to one library. Signal intensities range from white (low) to dark blue (high). Annotated ORF are represented as “box”. Original data described in [12]. e Strand-specific “heatmap” visualization of the paired-end total RNA-seq signal along the HOTAIR locus in MCF-7, HeLa-S3 and NHLF cell lines. Annotated transcripts and exons are represented as “arrow” and “rectangle”. Original data from the ENCODE project described in [13]