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For compatibility with the rhAmpSeq CRISPR Data Analysis Tool, we recommend submitting the targets of interest to the rhAmpSeq Design Tool as a 6-column BED file that includes the following information: chromosome, start, stop, desired name, mismatch # (or a 0), and strand (+ or –).
You can use the rhAmpSeq CRISPR Data Analysis Tool user guide for further information about input file formatting.