What does it mean when ICE reports "no alignment found between sample files"?
In order for the ICE tool to accurately interpret and analyze the edited trace file relative to the control file, it must be able to align the two traces by base call. This allows the tool to compare the two traces base-by-base to determine differences and potential indel patterns.
What is causing the error?
It is possible that the ICE tool is unable to find alignment between the edited and control files if the traces are from different genomic loci.
What can I do to fix these issues?
Verify that the same PCR primers and sequencing primers were used for both the control and edited samples. You may also use a BLAST search to determine if both sequences map to the same genomic location.
If the problem persists, please contact firstname.lastname@example.org with the following information:
- Url link to the analysis results if available
- Control and edited sample files with a description of which control file correspond to which edited file
- Guide sequence(s) and which control/edited file pair it corresponds to
- screenshots of any error messages or relevant details.