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. Author manuscript; available in PMC: 2025 Dec 13.
Published in final edited form as: Nat Protoc. 2024 Dec 15;20(6):1546–1583. doi: 10.1038/s41596-024-01090-z

Table 4.

Parameters for CRISPRessoBatch

Parameter Calls Purpose
--batch_settings e.g. batch_file.txt Specifies the fastq files to be analysed
-a [insert unedited sequence] Specifies the reference amplicon sequence
-e [insert edited sequence] Specifies the expected edited amplicon sequence
-g sgRNA spacer sequence
-q 30 Minimum q-score of a read for analysis, all below are discarded
-qwc Specify where in the amplicons is the editing window expected
--discard_indel_reads TRUE Discards reads containing indels, but counts the number of times this occurs. This is a convenient way to calculate the occurrence of indels downstream. However the user can omit this parameter (the default is FALSE) if they desire more detailed analysis of the types of indels occurring.