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Figure 4 | BMC Genomics

Figure 4

From: Tangram: a comprehensive toolbox for mobile element insertion detection

Figure 4

Illustration of RP and SR detection methods. The top panel demonstrates our RP MEI detection method. The blue line with orange box represents a sample genome with an MEI. Each pair of red arrows represent a read pair aligned to this genome. For RP method, we collect those repairs that one mate aligned uniquely to the genome the other mate aligned into the inserted ME. By clustering those uniquely aligned mates (green dashed boxes) we can estimate the insertion location. The type of inserted element is provided by MOSAIK aligner (ZA tags). The breakpoint confidence interval is given by the distance between two uniquely aligned mates that are closest to the real breakpoint. For SR method, the bottom panel, we collect those read pairs that one mate is uniquely aligned to the genome and the other mate is either unaligned or soft-clipped. The unaligned or soft-clipped read will be split into two segments: one of them will be aligned back to the normal human genome reference and the other segment will be aligned to the ME reference (blue box). The breakpoint can be determined by the alignment location of the first segment.

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