Digenome-sequencing

Genome-wide profiling of off-target effects.

Digenome-seq is an in vitro nuclease-digested whole-genome sequencing to profile genome-wide nuclease off-target effects in cells. This in vitro digest yields sequence reads with the same 5' ends at cleavage sites that can be computationally identified by Digenome-seq program. Thanks to Emscripten, this web version of Digenome-seq program completely runs on the client-side so that large amounts of sequencing data do not need to be uploaded to the server.

Please input your data in below form, or you can download a standalone version of this tool here. Also you can try this tool with an example data. Please check example protocol of Digenome-seq experiment in help page.

Sequencing Data

Please select a nuclease-treated and a control BAM file (which contains mapped reads against reference genome). The BAM files need to be coordinate-sorted.

Nuclease-treated BAM file

Control BAM file (optional) [?]

Reference genome (retrieved from Ensembl):

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Nuclease Information

Cleavage type

Blunt end 5' Sticky end (1 overhang) 5' Sticky end (2 overhang) 5' Sticky end (3 overhang) 5' Sticky end (4 overhang) 5' Sticky end (5 overhang) 5' Sticky end (6 overhang) 5' Sticky end (7 overhang) 5' Sticky end (8 overhang) 5' Sticky end (9 overhang) 5' Sticky end (10 overhang) 5' Sticky end (11 overhang) 5' Sticky end (12 overhang) 3' Sticky end (1 overhang) 3' Sticky end (2 overhang) 3' Sticky end (3 overhang) 3' Sticky end (4 overhang) 3' Sticky end (5 overhang) 3' Sticky end (6 overhang) 3' Sticky end (7 overhang) 3' Sticky end (8 overhang) 3' Sticky end (9 overhang) 3' Sticky end (10 overhang) 3' Sticky end (11 overhang) 3' Sticky end (12 overhang)

e.g.) Cas9: blunt end, AsCpf1, LbCpf1: 3 overhang (5'), FnCpf1: 5 overhang (5'), ZFN: 4 overhang (5'), TALEN: 6 overhang (5')

Target sequence(s), one sequence per line (optional, 5' to 3'):

Filtering Options

Minimum mapping quality for bam reads

Minimum number of forward reads with same 5' ends

Minimum number of reverse reads with same 3' ends

Minimum depth at each position

Minimum ratio at each position

Minimum cleavage score [?]

Run digenome-seq

In collaboration with: