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Old 05-26-2009, 01:47 AM   #2
Location: Oslo, Norway

Join Date: Nov 2008
Posts: 415

Reads are quality trimmed before assembly, the new start and stop are the left and right clipping points. Usually, the left (5') side is never trimmed (beyond the first four bases that are common for all reads).

Trim values can be changed using the sfffile command, check the manual.
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