FAQs
- Does the GE Pipeline go through QC checks initially? Can anything cause the pipeline to fail during the initial stages?
- Will I see any difference in my result on the web version (GUI) versus the On-premise versions (USB and server)?
- Can my % edited cells and % edited alleles be directly compared across my samples?
- What normalization method is used for Protein expression in the “On-target editing status vs. Protein Expression” plot?
- Why do I see many low-frequency variants in the “On-target variant distribution” plot for my negative control sample?
- What size distribution of indels does the report show?
- What are the recommended values/ ranges for the metrics on the Summary tab?
- What are the definitions of the metrics on the Summary tab?
- How do I distinguish between variants (e.g., SNVs) present in my cells (prior to editing) and actual edits?
- Should I analyze a negative control (unedited sample)?
- Does the GE Pipeline support Knockins/Homology-Directed Repair analysis?
- When should I generate a ‘BE’ report versus a ‘KO’ report?
- Is there a minimum number of cells with a particular variant/edit to call something a true positive vs. a false positive?
- When comparing results with ICE (or other bulk CRISPR editing tools) which metric should be used to compare editing efficiency?
- Do we have any tools to analyze the new h5 file format?
- What files would be the most important for troubleshooting if my results don't match my expectations?
- Does the GE Pipeline go through QC checks initially? Can anything cause the pipeline to fail during the initial stages?
- Can I change the default variant filters and how were these filters determined?
- I used the wrong “report type” when processing my sample, do I have to run the entire pipeline again?
- What is the average run time of the GE Pipeline?
- Can I run the GE Pipeline with V2 chemistry data?
- Is the analysis compatible with different gene editors (e.g., TALENs, ZFNs, CRISPR) & base editors.
- Are there limitations to the size of the custom panel?
- Are there limitations to the types of edits one can analyze?
- Can the GE Pipeline be used to analyze base editing and knockout approaches in the same sample?
- Will the GE analysis work with low cell inputs?
- What is the final list of output files?