| --trim-5 | Length of trimming the 5’ of the reads, default AUTO (MAGeCK will automatically determine the trimming length). |
| --sgrna-len | Length of the sgRNA. Default AUTO (MAGeCK will automatically determine the sgRNA length. Only use this if users turn on the “--unmapped-to-file” option. |
| --count-n | Count sgRNAs with Ns. By default, sgRNAs containing N will be discarded. |
| --unmapped-to-file | Save unmapped reads to file, with sgRNA lengths specified by --sgrna-len option. |
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