Override Cycles
The OverrideCycles mask elements are semicolon separated. For example:
OverrideCycles,U7N1Y143;I8;I8;U7N1Y143
DRAGEN supports flexible UMI processing during BCL conversion to support more third-party assays, including UMI sequences in index reads and multiple UMI regions per read. UMI sequences are trimmed from FASTQ read sequences and placed in the sequence identifier for each read, as normal.
The following are examples of OverrideCycles settings using 2x151 reads:
|
Setting |
Description |
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|---|---|---|---|---|---|---|---|---|---|---|
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OverrideCycles,U7N1Y143;I8;I8;U7N1Y143 |
UMI is composed of the first 7 bp of each genomic read, linked by 1 bp of ignored sequence, and is the format for Illumina nonrandom UMIs, used in the following products:
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OverrideCycles,Y151;I8;U10;Y151 |
Index Read 2 is a 10 bp UMI, and is the format for Agilent XT HS. |
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|
OverrideCycles,Y151;I8U9;I8;Y151 |
Index Read 1 contains both an index and a 9 bp UMI, and is the format for IDT Dual Index Adapters with UMIs. |
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|
OverrideCycles,U3N2Y146;I8;I8;U3N2Y146 |
UMI is composed of the first 3 bp of each genomic read, linked by 2 bp of ignored sequence, and is the format for UMIs in SureSelect XT HS 2 and IDT xGen Duplex Seq Adapter. |
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OverrideCycles,Y151;I8;I8;U10N12Y127 |
UMI is at the beginning of Read 2, attached with a linker sequence of length 12. |
