JACKIE (Jackie and Albert’s Comprehensive K-mer Instances Enumerator) scans the genome and enumerate all potential target sequences for ZFP, TALE or CRISPR and output their copy number and locations, and off-target counts

Publication:  

Zhu, J.J., Cheng, A.W. (2022) The CRISPR Journal doi: 10.1089/crispr.2022.0042 “JACKIE: Fast enumeration of genome-wide single- and multi-copy CRISPR target sites and their off-target numbers. ”

Source code and binaries: https://github.com/albertwcheng/JACKIE2

JACKIE.queryDB GUI Mac App: JACKIE.queryDB.GUI.app.zip

Human hg38 CRISPR/SpCas9 20mer+NGG datasets and UCSC Genome Browser sessions:

all (219,903,423) one-copy sgRNA binding sites with their off-target counts up to 3 mismatches [UCSC Genome Browser][Download bigBed][Download bed.gz file][Download AutoSql file for bed field definition][Generate JACKIE.queryDB command]

One-copy sgRNA binding sites with no off-target up to 3 mismatches [UCSC Genome Browser][Download bigBed][Download bed.gz file][Download AutoSql file for bed field definition][Generate JACKIE.queryDB command]

multi-copy (2+) <=50kb gRNA clusters with their off-target counts up to 3 mismatches [UCSC Genome Browser][Download bigBed][Download bed.gz file][Download AutoSql file for bed field definition] [Generate JACKIE.queryDB command]

all potential non-overlapping same-chromosome sgRNA binding sites in extended bed format [Download]

all potential sgRNA binding sites in bed format [Download]

Precomputed SeqSpace – hg38 20-mer CRISPR-SpCas9 NGG-PAM SeqSpace for JACKIE.countSeqNeighbors [Download]

Precomputed prefixed SeqSpace set – hg38 20-merCRISPR-SpCas9 NGG-PAM SeqSpace for JACKIE.countSeqNeighbors.prefixed [Download]

Precomputed SeqCountDatabase set – hg38 20-mer CRISPR-SpCas9 NGG-PAM 3-bit SeqCountDatabase for JACKIE.countOffSites [Download]

Mouse mm10 CRISPR/SpCas9 20mer+NGG datasets and UCSC Genome Browser sessions:

CRISPR/SpCas9

all (204,217,558) one-copy sgRNA binding sites with their off-target counts up to 3 mismatches [UCSC Genome Browser][Download bigBed][Download bed.gz file][Download AutoSql file for bed field definition][Generate JACKIE.queryDB command]

One-copy sgRNA binding sites with no off-targets up to 3 mismatches [UCSC Genome Browser][Download bigBed][Download bed.gz file][Download AutoSql file for bed field definition][Generate JACKIE.queryDB command]

multi-copy (2+) <=50kb gRNA clusters with their off-target counts up to 3 mismatches [UCSC Genome Browser ][Download bigBed][Download bed.gz file][Download AutoSql file for bed field definition][Generate JACKIE.queryDB command]

all one-copy sgRNA binding sites in bed format [Download]

all potential non-overlapping same-chromosome sgRNA binding sites in extended bed format [Download]

all potential sgRNA binding sites in bed format [Download]

Human hg38 ZFP datasets and UCSC Genome Browser sessions:

one-copy 18mer ZFP sites without 1-mismatch or 2-mismatch off-target matches [Open][Download BigBed]

one-copy 18mer ZFP sites without 1-mismatch off-target matches [Open][Download BigBed]

all one-copy 18mer ZFP sites [Open][Download BigBed]

Human hg38 20-mer no PAM restriction only positive strand UCSC Genome Browser sessions and bigbed:

all one-copy 20-mer (no PAM-restriction) +strand sites overlapping refGenes with their genomewide off-targets up to 3 mismatches  [Open][Download BigBed]