PiPipes: A set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome-and CAGE-seq, ChIP-seq and genomic DNA sequencing

Bioinformatics

Volumn 31, Issue 4, 2015, Pages 593-595

  Han, Bo W ^a   Wang, Wei ^a   Zamore, Phillip D ^a   Weng, Zhiping ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

METAZOA;

DROSOPHILA PROTEIN; RNA; SMALL INTERFERING RNA; TRANSPOSON;

ANIMAL; BIOLOGY; CHROMATIN IMMUNOPRECIPITATION; DNA SEQUENCE; DROSOPHILA MELANOGASTER; FEMALE; GENE EXPRESSION REGULATION; GENETICS; GENOME; GENOMICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; OVARY; PROCEDURES; PROTEIN DEGRADATION; SEQUENCE ANALYSIS; SOFTWARE; TRANSPOSON;

ANIMALS; CHROMATIN IMMUNOPRECIPITATION; COMPUTATIONAL BIOLOGY; DNA TRANSPOSABLE ELEMENTS; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; FEMALE; GENE EXPRESSION REGULATION; GENOME; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; OVARY; PROTEOLYSIS; RNA; RNA, SMALL INTERFERING; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84928998881     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu647     Document Type: Article

References (18)

1. Anders, S. et al. (2014) HTSeq-A Python framework to work with high-throughput sequencing data. Bioinformatics, 31, 166-169.
2. Brennecke, J. et al. (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell, 6, 1089-1103.
3. Chen, K. et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods, 9, 677-681.
4. Dobin, A. et al. (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 1, 15-21.
5. Grabherr, M.G. et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol., 7, 644-652.
6. Hormozdiari, F. et al. (2010) Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics, 12, i350-i357.
7. Keane, T.M. et al. (2013) RetroSeq: transposable element discovery from next-generation sequencing data. Bioinformatics, 3, 389-390.
8. Khurana, J.S. et al. (2011) Adaptation to P element transposon invasion in Drosophila melanogaster. Cell, 7, 1551-1563.
9. Luteijn, M.J. and Ketting, R.F. (2013) PIWI-interacting RNAs: from generation to transgenerational epigenetics. Nat. Rev. Genet., 8, 523-534.
10. Pohl, A. and Beato, M. (2014) bwtool: a tool for bigWig files. Bioinformatics, 11, 1618-1619.
11. Reuter, M. et al. (2011) Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing. Nature, 7376, 264-267.
12. Roberts, A. and Pachter, L. (2013) Streaming fragment assignment for real-time analysis of sequencing experiments. Nat. Methods, 1, 71-73.
13. Sienski, G. et al. (2012) Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression. Cell, 5, 964-980.
14. Trapnell, C. et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 5, 511-515.
15. Trapnell, C. et al. (2013) Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol., 1, 46-53.
16. Zhang, H. et al. (2013) RCircos: an R package for Circos 2D track plots. BMC Bioinformatics, 14, 244.
17. Zhang, Y. et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.
18. Zhuang, J. et al. (2014) TEMP: a computational method for analyzing transposable element polymorphism in populations. Nucleic Acids Res., 11, 6826-6838.