Tools and best practices for retrotransposon analysis using high-throughput sequencing data

被引:0
作者
Aurélie Teissandier
Nicolas Servant
Emmanuel Barillot
Deborah Bourc’his
机构
[1] Institut Curie,MINES ParisTech
[2] PSL Research University,undefined
[3] INSERM U900,undefined
[4] PSL Research University,undefined
[5] INSERM U934,undefined
[6] CNRS UMR 3215,undefined
来源
Mobile DNA | / 10卷
关键词
Retrotransposon; High-throughput sequencing; Data analysis; Mapping; Quantification;
D O I
暂无
中图分类号
学科分类号
摘要
引用
收藏
相关论文
共 125 条
[1]  
Platt RN(2018)Mammalian transposable elements and their impacts on genome evolution Chromosom Res 26 25-43
[2]  
Vandewege MW(2011)Repetitive elements may comprise over two-thirds of the human genome PLoS Genet 7 e1002384-5285
[3]  
Ray DA(2003)Hot L1s account for the bulk of retrotransposition in the human population Proc Natl Acad Sci U S A 100 5280-1685
[4]  
de Koning APJ(2001)A novel active L1 retrotransposon subfamily in the mouse Genome Res 11 1677-46
[5]  
Gu W(2011)Repetitive DNA and next-generation sequencing: computational challenges and solutions Nature Reviews Genetics 13 36-104
[6]  
Castoe TA(2016)Alternative computational analysis shows no evidence for nucleosome enrichment at repetitive sequences in mammalian spermatozoa Dev Cell 37 98-771
[7]  
Batzer MA(2015)Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi’s genomic targets still not identified Dev Cell 32 765-3177
[8]  
Pollock DD(2012)A, rung J, Brazma a, Marioni JC. Tools for mapping high-throughput sequencing data Bioinformatics 28 3169-9
[9]  
Brouha B(2016)Simulation-based comprehensive benchmarking of RNA-seq aligners Nat Methods 4 1-16
[10]  
Schustak J(2014)Comparison of mapping algorithms used in high-throughput sequencing: application to ion torrent data BMC Genomics 15 1-359