FAQ

My organism’s genome isn’t available on CHOPCHOP. How do I add it?

Please follow the instructions on the submissions page. We usually add new genomes around once per month.

There is a new assembly for my favorite organism. Can you update the current assembly on CHOPCHOP?

If we already support your organism of interest, you can email Tessa with a link to the new assembly and we’ll add it.

I want to run batches of organisms using CHOPCHOP. Do you have a command-line tool?

Yes, we have a command-line version of CHOPCHOP here. If you have questions about this, please email Kornel

I keep getting errors. I don’t understand why. Or I think results are erroneous...

Please send the URL link to your error page e.g. chopchop.cbu.uib.no/results/124145141.41241 and some description why do you think what you see is incorrect to Kornel

Last year I was targeting my favorite gene with CHOPCHOP, and now I get a “Gene ID not found” error message.

RefSeq/Ensembl/GENCODE periodically release new gene sets, and we update CHOPCHOP with the latest releases. Usually only new IDs are added, but sometimes old IDs get dropped or changed based on RefSeq/Ensembl curation. If you can’t find your gene ID, try searching for it in the UCSC Genome Browser. You may find an alternative ID name that you can use in CHOPCHOP.

How do I acknowledge CHOPCHOP in my work?

If you use our tool please cite at least the latest paper:

Labun, K., Montague, T. G., Krause, M., Torres Cleuren, Y. N., Tjeldnes, H., & Valen, E. CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing. Nucleic Acids Research (2019).

and if you can:

Labun, K., Montague, T. G., Gagnon, J. A., Thyme, S. B. & Valen, E. CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering. Nucleic Acids Res. 44, W272–6 (2016).

and:

Montague, T. G., Cruz, J. M., Gagnon, J. A., Church, G. M. & Valen, E. CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res. 42, W401–7 (2014).

Any other queries

Genome questions: email Tessa
Web tool + command-line tool functionality: email Kornel