What does it mean when ICE reports "guide not found in sequence"
The guide RNA sequence which you provide to the tool must be present in the control sanger sequence file. If the tool is unable to loacte the provided guide sequence in the control file, then it is unable to predict the cutsite and associated indel patterns.
What is causing the error?
There are several reasons why the tool may recognize this error:
1) The incorrect guide sequence may have been input into the tool
2) The incorrect region of the genome may have been amplified and/or sequenced
3) The quality of the .ab1 file may be too low for the tool to recognize the guide sequence or the region around it.
What can I do to fix these issues?
1) Verify that you have entered the correct 17-23 nucleotide guide sequence, excluding the PAM site.
2) Verify that the guide sequence you entered is present in the control .ab1 file. This can be done by simply opening the .ab1 file and using the "command+F" function to search for the entered guide sequence.
3) Check that the quality of the .ab1 file is sufficient. (See the "What can I do to fix these issues" section in the "Quality Score too low" Help Article)
If the problem persists, please contact email@example.com with the following information:
- Url link to the analysis results if available
- Control and edited sample files with a description of which control file corresponds to which edited file
- Guide sequence(s) and which control/edited file pair it corresponds to
- screenshots of any error messages or relevant details.