Bedshift: perturbation of genomic interval sets.
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ABSTRACT:
SUBMITTER: Gu A
PROVIDER: S-EPMC8379854 | biostudies-literature | 2021 Aug
REPOSITORIES: biostudies-literature
Publications
Bedshift: perturbation of genomic interval sets.
Gu Aaron A Cho Hyun Jae HJ Sheffield Nathan C NC
Genome biology 20210820 1
Functional genomics experiments, like ChIP-Seq or ATAC-Seq, produce results that are summarized as a region set. There is no way to objectively evaluate the effectiveness of region set similarity metrics. We present Bedshift, a tool for perturbing BED files by randomly shifting, adding, and dropping regions from a reference file. The perturbed files can be used to benchmark similarity metrics, as well as for other applications. We highlight differences in behavior between metrics, such as that t ...[more]
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