Is it possible to store chromatograms from Sequence in different subdirectories?


Yes, but the sequence allows the chromatograms to be stored only in the subdirectories of current project directory. The path will be specified in the File Name column as a relative path only, i.e for C:\Clarity\DataFiles\Work1\Data\MyProject\ChromatogramName you have to set the filename as MyProject\ChromatogramName.

This limitation is necessary to allow the opening chromatograms from sequence and to perform complete reprocess of the sequence from the Batch dialog accessible using the Analysis - Batch command from the Instrument window.