Fig. 2

Schematic view of the competitive mapping analyses. FASTQ files represent ‘raw’ sequencing files and BAM files represent alignments to a reference genome. Color boxes indicate different types of data: blue, files that need further processing; red, discarded data; and green, data for downstream analyses. a Schematic view of the analyses performed in this manuscript. An example using a mammoth sample is shown. First, normal mapping to the elephant, human and dog references to check for endogenous content as well as non-target and human contamination in the sequencing files. Second, competitive mapping to a concatenated reference of an elephant and human to detect human contamination in the alignments. Third, normal mapping human data to the elephant reference to check that the human contaminat sequences map preferentially to conserved regions of the genome. b Schematic view of a typical competitive mapping pipeline using a mammoth sample as example. After competitive mapping, only the sequences mapping to the elephant part of the concatenated reference will be used for downstream analyses