GT-Scan2 identifies optimal CRISPR-Cas9 targets in the human genome by combining information about the chromatin environment and sequence of the target site. Information about the chromatin environment is collected from the Roadmap Epigenomics Project, providing detailed epigenetic maps of over 100 different human tissues. The contribution of the target sequence is determined by combining the results of two publically available models: WU-CRISPR and sgRNA Scorer. By combining these different sources of information, GT-Scan2 is able to more reliably identify high activity CRISPR-Cas9 target sites.

Submission form


When completing the form, it is important that the position of the first nucleotide in your Genomic sequence matches the first value you specify in Chromosome and Region. The second value in Region is optional.

Alternatively, you can specify both values in Region and click Fetch sequence to have GT-Scan2 download the Genomic sequence for you.

The Genomic region should be an unspliced region of DNA, containing only [A T C G N].

Finally select one of the samples for Roadmap. You can view more information about these datasets at the Roadmap Epigenomics Project page.


The results page for each job displays the predicted activity and number of potential off-targets for each candidate target.
The table will refresh automatically (every five seconds). Depending on the specified job parameters, it may take up to a few minutes for the table to complete.
You can view the following example output here.

Results target table

Each row represents a candidate target from the input genomic sequence. Targets are ranked primarily by their predicted activity, followed by the number of potential off-targets they have.

  • The first two columns display the position and direction of each candidate target in the genomic sequence.
  • The third column displays thei nucleotide sequence.
  • The fourth column displays the predicted activity. This is a binary value (High or Low), derived from certain properties of the candidate target
  • The fifth to eigth columns display the total number of potential off-targets throughout the genome, where a potential off-target is an identical sequence to the candidate target at the given Hamming distance for each column.

Predicted Activity

The predicted activity is calculated from the output of sgRNA Scorer, WU-CRISPR and intersects with the Roadmap Epigenomics Data. To view the output of each of these processes, click the More details button.

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