Originally posted by simonandrews
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The v1.8 User guide gives the following scenarios
Bcl Conversion/Demultiplexing Examples
Bcl conversion and demultiplexing support four scenarios:
1)Multiplexed samples present, with sample sheet.
Reads are placed within the directory structure specified by the sample sheet, based
on the index and lane information. Reads for which the index sequence was
ambiguous will be placed in a project directory called Undetermined_indices,
unless the sample sheet specifies a specific sample and project for reads without
index in that lane.
2)Multiplexed and non-multiplexed samples present, with sample sheet.
Reads are placed within the directory structure specified by the sample sheet, based
on the index and lane information. Reads containing ambiguous or no barcodes
will be placed in a project directory called Undetermined_indices, unless the sample
sheet specifies a specific sample and project for reads without index in that lane.
3)No multiplexed samples present, with sample sheet.
Reads are placed within the directory structure directed by the sample sheet, based
on the lane information.
4)No multiplexed samples present, without sample sheet.
Reads are placed in a project directory named after the flow cell, and sample
directories based on the lane number.
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