|Interface||Command line interface|
|Restrictions to use||None|
|Input format||BED, BAM, VCF, GFF|
|Output format||BED, BAM, VCF, GFF, BAI|
|License||GNU General Public License version 2.0|
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- person_outline Aaron R. Quinlan <>
[…] of 3′ utrs with 3′ ends within 24 nt of each other to produce a non-redundant set of isoforms. all genomic interval operations were performed using pybedtools . sequences were extracted using bedtools getfasta ., transcript-level expression of 3′ utrs was measured using sailfish v0.8.0  and our curated reference library of 3′ utr sequences. to quantify the relative usage of 3′ utr […]
[…] ns, reads with more than 80% adenines, and reads where the last nucleotide is adenine. to annotate and quantify poly(a) sites, reads overlapping the polyasite (hg19) database were quantified using bedtools intersect (with options –s, −wa, and –c) , forming poly(a) site clusters. to ensure that all reads that mapped near a poly(a) site cluster were counted, we extended clusters less than 30 […]
[…] and the odds-ratio ≥2 (≤0.5)., adapter trimming and mapping to human and hsv-1 genomes was performed as described for the 4su-seq data. bam files with mapped reads were converted to bed format using bedtools  and ocrs were determined from these bed files using f-seq with default parameters . no filtering of ocrs was performed. assignment of ocrs to gene promoters was performed using […]
[…] were visualized in the ucsc genome browser (https://genome-store.ucsc.edu/). all libraries were normalized to the number of mapped reads per million (rpm) and bedgraph files were generated using bedtools (v2.20.1) (quinlan and hall, 2010). for log2 ratio tracks α-hp1 chip values were divided by input values and log2-transformed using bedtools (v2.20.1) (quinlan and hall, 2010). within […]
[…] the levenshtein distance was calculated in python using the distance module v0.1.3. analysis details can be found in jupyter notebook pst_104e_v12_post_allele_analysis submission_21092017., we used bedtools v2.25.0 (94) and the python module pybedtools (95) to perform various genome analysis tasks. this included the calculation of nearest neighbors using the closest function. details […]
In comparison, however, Homer is better if you want to intersect further files because it gives more details, ideal to create a Venn diagram !
A big plus of bedtools : tools are very well documented, with schemes ! I like: "shuffle" to randomly relocate peaks, to test significance of a pathway enrichment for example !