How to generate FASTQs for a run without specifying indexes using BCL Convert
To generate FASTQs for a run using BCL Convert such that all reads from the run go to a single sample's FASTQ files (Read1 AND Read2 for paired end runs and Read 1 for single read runs):
Specify a single unindexed sample in the [Data] and [BCLConvert_Data] sections.
Include the appropriate OverrideCycles settings to mask the indexes.
For example, if a 151\*10\*10\*151 run is to be processed such that all reads from the run are to go to a single sample, a suitable sample sheet for BCL Convert must include the following.
[BCLConvert_Settings]
OverrideCycles,Y151;N10;N10;Y151
[BCLConvert_Data]
Sample_ID,index,index2,Sample_Project
Sample_1,,,Sample_Project
To create FASTQ files for the Index reads in this scenario, include a placeholder index in the sample sheet so all reads will go to the Undetermined FASTQ files (Read1, Index1, Index2, and Read2). For the aforementioned run, a suitable sample sheet must include a pair of placeholder indexes (two polyA sequences, for instance) and no OverrideCycles, as follows.
[BCLConvert_Settings]
CreateFastqForIndexReads,1
[BCLConvert_Data]
Sample_ID,index,index2,Sample_Project
Sample_1,AAAAAAAAAA,AAAAAAAAAA,Sample_Project
As an extension, if this scenario ("unindexed" demultiplexing and indexes to be output to FASTQ files) only applies for a single lane of a run (for applicable sequencers), then a lane column must be included in the [BCLConvert_Settings] and [BCLConvert_Data] sections.
[BCLConvert_Settings]
CreateFastqForIndexReads,1
[BCLConvert_Data]
Lane,Sample_ID,index,index2,Sample_Project
2,Sample_1,AAAAAAAAAA,AAAAAAAAAA,Sample_Project
With the above example, all reads from lane 2 will be output to the 4 Undetermined FASTQ files (Read1, Read2, Index1 and Index2).
Note:
Starting with BCL Convert v4.0.3, BCL Convert has a dedicated flag, --no-sample-sheet true, that outputs all reads to a single sample called Undetermined.
Adapter trimming and other settings included in the sample sheet are ignored, and Index FASTQ files cannot be generated with this option. The default value of this flag is False/false.
More information is available in the BCL Convert online help page.
For any feedback or questions regarding this article (Illumina Knowledge Article #7493), contact Illumina Technical Support techsupport@illumina.com.
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