The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
BEDTools: The Swiss‐Army Tool for Genome Feature Analysis
Open accessAbstract
Technological advances have enabled the use of DNA sequencing as a flexible tool to characterize genetic variation and to measure the activity of diverse cellular phenomena such as gene isoform expression and transcription factor binding. Extracting biological insight from the experiments enabled by these advances demands the analysis of large, multi‐dimensional datasets. This unit describes the use of the BEDTools toolkit for the exploration of high‐throughput genomics datasets. Several protocols are presented for common genomic analyses, demonstrating how simple BEDTools operations may be combined to create bespoke pipelines addressing complex questions. Curr. Protoc. Bioinform. 47:11.12.1‐11.12.34. © 2014 by John Wiley & Sons, Inc.
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The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
The variant call format and VCFtools
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr330 · Cited by 16,200
The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877
Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716
Exome sequencing identifies the cause of a mendelian disorder
Ng, S. B., Buckingham, K. J., Lee, C., Bigham, A. W., Tabor, H. K., Dent, K. M., Huff, C. D., Shannon, P. T., Jabs, E. W., Nickerson, D. A., et al. (2010) · Nature Genetics · doi:10.1038/ng.499 · Cited by 1,957
BigWig and BigBed: enabling browsing of large distributed datasets
Kent, W. J., Zweig, A. S., Barber, G., Hinrichs, A. S., & Karolchik, D. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq351 · Cited by 1,310
Exploring Massive, Genome Scale Datasets with the GenometriCorr Package
Favorov, A., Mularoni, L., Cope, L. M., Medvedeva, Y., Mironov, A. A., Makeev, V. J., & Wheelan, S. J. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002529 · Cited by 183
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SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation
Shen, W., Le, S., Li, Y., & Hu, F. (2016) · PLOS ONE · doi:10.1371/journal.pone.0163962 · Cited by 3,380
Howard, D. M., Adams, M. J., Clarke, T.-K., Hafferty, J. D., Gibson, J., Shirali, M., Coleman, J. R. I., Hagenaars, S. P., Ward, J., Wigmore, E. M., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-018-0326-7 · Cited by 2,565
Wenger, A. M., Peluso, P., Rowell, W. J., Chang, P.-C., Hall, R. J., Concepcion, G. T., Ebler, J., Fungtammasan, A., Kolesnikov, A., Olson, N. D., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0217-9 · Cited by 1,841
Innate immune memory in the brain shapes neurological disease hallmarks
Wendeln, A.-C., Degenhardt, K., Kaurani, L., Gertig, M., Ulas, T., Jain, G., Wagner, J., Häsler, L. M., Wild, K., Skodras, A., et al. (2018) · Nature · doi:10.1038/s41586-018-0023-4 · Cited by 956
Acetylation of Cytidine in mRNA Promotes Translation Efficiency
Arango, D., Sturgill, D., Alhusaini, N., Dillman, A. A., Sweet, T. J., Hanson, G., Hosogane, M., Sinclair, W. R., Nanan, K. K., Mandler, M. D., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.030 · Cited by 862
Metadata
- Authors
- Quinlan, A. R.
- Venue
- Current Protocols in Bioinformatics
- Publisher
- Wiley
- Published
- 2014-09
- Volume
- 47
- Issue
- 1
- Pages
- 11.12.1-34
- ISSN
- 1934-3396 (ISSN-L)
- 1934-340X
- OpenAlex
- W2136430672
- Cited by
- 2,370
- References
- 9
- FWCI
- 30.42
- Type
- journal article
- Language
- en
- Open access
- green
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