Fig. 1
From: cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries
Workflow of cDNA-detector. A Schematic illustrating the source of intentional or contaminant cDNA reads in sequencing experiments. Vectors (grey) with cDNA (red) are amplified in the library preparation process and sequenced together with the experiment. Upon alignment of reads, cDNA-derived reads (red boxes) map to the respective gene locus in the genome, along with true signal reads (blue). Textured red read segments indicate sequence not mapping to the genome and “clipped” by the alignment algorithm. B Overview of the two main components of the cDNA-detector algorithm, “detect” and “decontaminate”. C ATAC-seq experiment from TCGA before (pink) and after (green) removal of vector-introduced KRAS. For comparison, an uncontaminated sample (grey) is shown. Boxes indicate contaminant signal over exons