Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks.
The most widely-used tools enable genome arithmetic: While each individual tool is designed to do a relatively simple task e. We have developed a fairly comprehensive tutorial that demonstrates both
Kvinna fros fast i marken basics, as well as some more advanced examples of how bedtools can help you in your research.
Please have a look. In addition, here are a few examples of how bedtools has been used for genome research. If you have interesting examples, please send them our way and we will add them to the list.
As of version 2. As you can see in the plots below, the speed and memory consumption scale nicely with sorted data as compared to the poor scaling for unsorted data.
The alignments have been converted to BED to facilitate comparisons to bedops. We compare to the bedmap --ec option because similar error checking is enforced by bedtools.
Such an analysis could be conducted with two, relatively simple bedtools commands. If you have questions, requests, or bugs to report, please email the bedtools mailing list. Navigation index next bedtools v2. Unless you use the -sorted option, bedtools currently does not support larger than Mb When using the -sorted option with files whose chromosomes are not lexicographically sorted e.
Coverage analysis for targeted DNA capture. Thanks to Stephen Turner.
Measuring similarity of DNase hypersensitivity among many cell types Extracting promoter sequences from a genome Comparing intersections among many genome interval files RNA-seq coverage analysis. Thanks to Erik Minikel.
Identifying targeted regions that lack coverage.
Thanks to Brent Pedersen. Making a master table of ChromHMM tracks for multiple cell types. Bedtools is a fast, flexible toolset for genome arithmetic. Quinlan and Neil Kindlon. Last updated on Dec 08, As you can see in the plots below, the speed and memory consumption scale nicely with sorted data as compared to the poor scaling for Kvinna fros fast i marken data.
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