Figure 1.

SeqOutBias overview and parameter definitions. (A) An enzymatic cleavage event that results in a blunt end can be detected by sequencing the upstream or downstream DNA (red bases). The hexamer sequence centered (red block) on the nick sites (dotted vertical lines) confers specificity; this parameter is referred to as the k-mer. The plus-offset and minus-offset parameters specify the nick site relative to the first position and last position of the k-mer. As opposed to specifying the immediate upstream base for the minus strand, we shift the base position by +1 to match the first position of the plus aligned read. (B) This panel illustrates the high-level overview of the inputs, intermediate files and output of the seqOutBias program and the computation steps that the program performs. The tallymer step indexes the reference sequence (FASTA) and computes mappability for the given read length. The seqTable step parses the reference sequence together with the mappability information to compute the k-mer that corresponds to each possible read alignment position. The tabulate step tallies the k-mer counts across the selected regions (or the full genome), as well as the k-mers corresponding to observed aligned reads (if a BAM file is supplied). At last, scale computes the genome-wide aligned read pile-ups, scaling sequence reads by the expected/observed k-mer frequency.