SraTailor: Graphical user interface software for processing and visualizing ChIP-seq data

Genes to Cells

Volumn 19, Issue 12, 2014, Pages 919-926

  Oki, Shinya ^a   Maehara, Kazumitsu ^a   Ohkawa, Yasuyuki ^a   Meno, Chikara ^a  

^a KYUSHU UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMATIN IMMUNOPRECIPITATION; COMPUTER INTERFACE; COMPUTER PROGRAM; DEVICES; DNA SEQUENCE; INFORMATION PROCESSING;

AUTOMATIC DATA PROCESSING; CHROMATIN IMMUNOPRECIPITATION; SEQUENCE ANALYSIS, DNA; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84910667093     PISSN: 13569597     EISSN: 13652443     Source Type: Journal    
DOI: 10.1111/gtc.12190     Document Type: Article

References (12)

1. Ang, Y.-S., Tsai, S.-Y., Lee, D.-F., Monk, J., Su, J., Ratnakumar, K., Ding, J., Ge, Y., Darr, H., Chang, B., Wang, J., Rendl, M., Bernstein, E., Schaniel, C. & Lemischka, I.R. (2011) Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell 145, 183-197.
2. Furey, T.S. (2012) ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat. Rev. Genet. 13, 840-852.
3. Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., Miller, W., Kent, W.J. & Nekrutenko, A. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 15, 1451-1455.
4. Goecks, J., Nekrutenko, A. & Taylor, J. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11, R86.
5. Langmead, B. & Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359.
6. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25.
7. Li, H. & Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760.
8. Li, H. & Durbin, R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595.
9. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. & Durbin, R. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079.
10. Quinlan, A.R. & Hall, I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842.
11. Robinson, J.T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E.S., Getz, G. & Mesirov, J.P. (2011) Integrative genomics viewer. Nat. Biotechnol. 29, 24-26.
12. Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W. & Liu, X.S. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137.