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Fig. 1 | BMC Genomics

Fig. 1

From: Next-generation sequencing-based detection of germline L1-mediated transductions

Fig. 1

TIGER approach. a L1-mediated transduction insertions are typically composed of flanking target site duplications (TSDs, purple triangles), L1 sequence and unique transduction sequence (TS) followed by a non-reference polyA tail. To detect such events in paired-end NGS data, candidate regions are chosen based on an overlap between L1 insertion loci, paired-ends indicative for an insertion of unique sequence copied from a distal locus (as evident from translocation (TL) supporting read pairs), and remapped single-anchored (SA) reads in the reference genome. b A combination of reads indicative for L1 insertion as well as unique duplicative sequence insertion and additionally single-anchored reads are used to discover L1-mediated transduction insertions. TL and SA read pairs are realigned to ensure correct placement onto the reference genome. Additional filtering steps are implemented for removal of low-confidence calls

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