Uploading your own reference library:

The reference library has to contain one column with the Gene name and another column with the gRNA/spacer sequence. Other columns could be included, such as a ranking score if applicable. The reference library has to be uploaded as a Tab Delimited Text File (.txt). We often prepare the reference libraries in excel and then save them as a Tab Delimited Text File. Keep in mind that excel can introduce (easily fixed) artefacts in a library by changing the name of genes, if excel e.g. interprets a name as a date (this happens for e.g. the Sept gene family).

As the Reference library has been successfully uploaded, Green Listed specifies that “The file has been uploaded and is ready to be processed”. Sometimes it can take a little while if the internet connection is not optimal, or the server is occupied. Still you need to await the confirmation before you press run.

As a reference library has been uploaded, define which column that contains gene ID, gRNA and, if applicable ranking. Note that the ranking option is only relevant if the reference library contains a ranking score (the GeCKOv2 does not).

If you press the Demo link you can download a short demo references library and see how it is formatted, as well as to test using it by following the instructions in the Demo tab. You can also download the formatted GeCKOv2 libraries used in the software under the GeCKOv2 info tab.

Several excellent reference libraries are presented in publications referred to in the reference list found in the “How to use” document.