BEDTools: a flexible suite of utilities for comparing genomic features
Citations
15,744 citations
Cites background from "BEDTools: a flexible suite of utili..."
...Interval queries are a recurring task in HTS analysis problems, and several libraries now offer solutions for different programming languages, including BEDtools (Quinlan and Hall, 2010; Dale et al., 2011) and IRanges/GenomicRanges (Lawrence et al....
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...Interval queries are a recurring task in HTS analysis problems, and several libraries now offer solutions for different programming languages, including BEDtools (Quinlan and Hall, 2010; Dale et al., 2011) and IRanges/GenomicRanges (Lawrence et al., 2013)....
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14,103 citations
Cites methods from "BEDTools: a flexible suite of utili..."
...Instead of using multiple levels of bins (Kent et al., 2002; Quinlan and Hall, 2010), the algorithm uses only one level of bins in combination with the feature blocks....
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...BEDTools is a popular tool for finding overlaps between genomic features that can be used to count overlaps between reads and features (Quinlan and Hall, 2010)....
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12,661 citations
8,197 citations
7,892 citations
Cites methods from "BEDTools: a flexible suite of utili..."
...To compare global patterns of chromatin accessibility, we identified variable peaks among the bulk ATAC-seq samples and computed the peak coverage of each pseudo-bulk scATAC-seq population using bedtools multicov [Quinlan and Hall, 2010]....
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References
45,957 citations
12,432 citations
"BEDTools: a flexible suite of utili..." refers methods in this paper
...BEDTools also includes utilities for extracting and masking FASTA sequences (Pearson and Lipman, 1988) based upon BED intervals....
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9,605 citations
"BEDTools: a flexible suite of utili..." refers methods in this paper
...Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format....
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2,071 citations
"BEDTools: a flexible suite of utili..." refers methods in this paper
...Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format....
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