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Transposable element detection from whole genome sequence data

Ewing, Adam D.·2015·Mobile DNA
DOI 10.1186/s13100-015-0055-3PMC PMC4696183
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Fig. 1 Read mapping patterns typically associated with insertion detection. Panel a shows the read mapping patterns versus a reference TE sequence (grey rectangle, top) and the mapping of the same reads to a reference genome sequence (orange rectangle, bottom). Reads are represented as typical paired-end reads where the ends of each amplicon are represented as rectangles and the un-sequenced portion of the amplicons are represented as bars connecting the rectangles. Reads informative for identifying TE insertion locations are indicated by dashed boxes, other read mappings to the TE reference are shown in light blue boxes. Within the informative reads, reads or portions of reads mapping to the TE reference are coloured blue, and mappings to the reference genome sequence are coloured yellow. The exact location of this example insertion is indicated by the red triangle and the dashed line. Assembly of the reads supporting the two junction sequences is indicated to the right of the ‘consensus’ arrow, one example with a TSD and one without. If a TSD is present, the insertion breakends relative to the reference genome are staggered, and the overlap of reference-aligned sequence corresponds to the TSD. If a TSD is not present (and no bases are deleted upon insertion), the junctions obtained from the 5' end and the 3' end of the TE reference will match exactly. Panel b shows a typical pattern of discordant read mappings across a genome - the colored segments in circle represent chromosomes, each black link indicates a discordant read mapping supporting an insertion at the position indicated by the red triangle. The endpoints not corresponding to the insertion site map to TE elements at various locations in the reference genome
Fig. 1 Read mapping patterns typically associated with insertion detection. Panel a shows the read mapping patterns versus a reference TE sequence (grey rectangle, top) and the mapping of the same reads to a reference genome sequence (orange rectangle, bottom). Reads are represented as typical paired-end reads where the ends of each amplicon are represented as rectangles and the un-sequenced portion of the amplicons are represented as bars connecting the rectangles. Reads informative for identifying TE insertion locations are indicated by dashed boxes, other read mappings to the TE reference are shown in light blue boxes. Within the informative reads, reads or portions of reads mapping to the TE reference are coloured blue, and mappings to the reference genome sequence are coloured yellow. The exact location of this example insertion is indicated by the red triangle and the dashed line. Assembly of the reads supporting the two junction sequences is indicated to the right of the ‘consensus’ arrow, one example with a TSD and one without. If a TSD is present, the insertion breakends relative to the reference genome are staggered, and the overlap of reference-aligned sequence corresponds to the TSD. If a TSD is not present (and no bases are deleted upon insertion), the junctions obtained from the 5' end and the 3' end of the TE reference will match exactly. Panel b shows a typical pattern of discordant read mappings across a genome - the colored segments in circle represent chromosomes, each black link indicates a discordant read mapping supporting an insertion at the position indicated by the red triangle. The endpoints not corresponding to the insertion site map to TE elements at various locations in the reference genomeCC BY · PubMed Central
Fig. 2 Intersections between somatic insertion detection methods. Overlap and non-overlap between insertion sites from reported in publications using the indicated software tools on the same data. The number of samples included in the comparison shared between the each pair of studies is indicated
Fig. 2 Intersections between somatic insertion detection methods. Overlap and non-overlap between insertion sites from reported in publications using the indicated software tools on the same data. The number of samples included in the comparison shared between the each pair of studies is indicatedCC BY · PubMed Central

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Metadata

Authors
Ewing, A. D.
Venue
Mobile DNA
Publisher
Springer Science and Business Media LLC
Published
2015-12
Volume
6
Issue
1
ISSN
1759-8753
DOI
10.1186/s13100-015-0055-3
PMC
PMC4696183
Cited by
155
References
6
Language
en
Licence
Funders
  • Australian Research Council (DE150101117)
  • Mater Foundation

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Ewing, A. D. (2015). Transposable element detection from whole genome sequence data. Mobile DNA. https://doi.org/10.1186/s13100-015-0055-3