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Copy file name to clipboardexpand all lines: doc/FAQ.md
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Yes, the LIGATION_SITE variable from the configuration file can contain multiple ligation motifs (comma separated).
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Regarding the Arima kit, as there is two restiction motifs (^GATC and G^ANTC), the possible ligation motifs should be GATCGATC,GANTGATC,GANTANTC,GATCANTC.
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Leading to 25 possible ligation motifs when the 'N' are replaced by 'A', 'C', 'G', 'T'.
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Since HiC-Pro version 2.11.3, 'N' base are automatically recognized.
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For older version, please specify all possible ligation motifs.
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