Settings Section
The software uses the settings section of the sample sheet to specify adapter trimming, cycle, UMI, and index options.
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Setting |
Description |
Default |
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AdapterRead1 |
The sequence of the Read 1 adapter to be masked or trimmed. To trim multiple adapters, separate the sequences with a plus sign (+) indicating independent adapters that must be independently assessed for masking or trimming for each read. Allowed characters: A, T, C, G. |
Not applicable |
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AdapterRead2 |
The sequence of the Read 2 adapter to be masked or trimmed. To trim multiple adapters, separate the sequences with a plus sign (+) indicating independent adapters that must be independently assessed for masking or trimming for each read. Allowed characters: A, T, C, G. |
Not applicable |
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AdapterBehavior |
Defines whether the software masks or trims Read 1 and/or Read 2 adapter sequence(s). When AdapterRead1 or AdapterRead2 is not specified, this setting cannot be specified.
|
trim |
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AdapterStringency |
The minimum match rate that triggers masking or trimming. This value is calculated as MatchCount / (MatchCount+MismatchCount). Accepted values are 0.5–1. The default value of 0.9 indicates that only reads with ≥ 90% sequence identity with the adapter are trimmed. |
0.9 |
|
Setting |
Description |
Default |
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BarcodeMismatchesIndex1
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The number of mismatches allowed for index1. Accepted values are 0, 1, or 2. |
1
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BarcodeMismatchesIndex2 |
The number of mismatches allowed for index2. Accepted values are 0, 1, or 2. |
1 |
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CreateFastqForIndexReads |
Specifies whether software will output fastqs for index reads. If index reads are defined as a UMI then fastqs for the UMI will be output (if TrimUMI is also set to 0). At least 1 index read must be specified in the sample sheet.
|
0 |
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MinimumTrimmedReadLength |
The minimum read length after adapter trimming. The software trims adapter sequences from reads to the value of this parameter. Bases below the specified value are masked with N. |
35
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MaskShortReads |
The minimum read length containing A, T, C, G values after adapter trimming. Reads with less than this number of bases become completely masked. If this value is less than 22, the default becomes the MinimumTrimmedReadLength. |
22
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OverrideCycles |
Specifies the sequencing and indexing cycles that should be used when processing the data. The following format must be used:
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Use reads as specified in the RunInfo.xml
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SoftwareVersion |
[Optional] Records the version of BaseSpace Sequence Hub intended to be used for conversion. Only supported by sample sheet V2. |
Not applicable |
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TrimUMI |
Specifies whether UMI cycles will be excluded from fastq files. At least one UMI is required to be specified in the Sample Sheet when this setting is provided.
|
1 |