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Mob DNA. 2019 Jul 10;10:29. doi: 10.1186/s13100-019-0172-5. eCollection 2019.

Paired-end mappability of transposable elements in the human genome.

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1School of Life Sciences, University of Nevada, Las Vegas, NV 89154 USA.
Nevada Institute of Personalized Medicine, Las Vegas, NV 89154 USA.


Though transposable elements make up around half of the human genome, the repetitive nature of their sequences makes it difficult to accurately align conventional sequencing reads. However, in light of new advances in sequencing technology, such as increased read length and paired-end libraries, these repetitive regions are now becoming easier to align to. This study investigates the mappability of transposable elements with 50 bp, 76 bp and 100 bp paired-end read libraries. With respect to those read lengths and allowing for 3 mismatches during alignment, over 68, 85, and 88% of all transposable elements in the RepeatMasker database are uniquely mappable, suggesting that accurate locus-specific mapping of older transposable elements is well within reach.


GEM; L1HS; Mappability; RNA-Seq; Transposon

Conflict of interest statement

Competing interestsThe authors declare that they have no competing interests.

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