| Behavior | Obsolete bcl2fastq/bcl2fastq2 Setting | New BCL Convert Setting |
|---|---|---|
| Designate the adapter sequences for Read 1 and Read 2 and specify the behavior as trim. | (Sample Sheet) Adapter, AGATCGGAAGAGCACACGTCTGAACTCCAGTCA OR TrimAdapter, AGATCGGAAGAGCACACGTCTGAACTCCAGTCA |
(Sample Sheet) AdapterRead1, AGATCGGAAGAGCACACGTCTGAACTCCAGTCA AND AdapterRead2, AGATCGGAAGAGCACACGTCTGAACTCCAGTCA |
| Designate the same adapter sequence for Read 1 and Read 2 and specify the behavior as mask. | (Sample Sheet) MaskAdapter, AGATCGGAAGAGCACACGTCTGAACTCCAGTCA |
(Sample Sheet) AdapterRead1, AGATCGGAAGAGCACACGTCTGAACTCCAGTCA AND AdapterRead2, AGATCGGAAGAGCACACGTCTGAACTCCAGTCA AND AdapterBehavior, mask |
| Designate the adapter sequences for Read 1 and Read 2 and specify the behavior as mask. | (Sample Sheet) MaskAdapter, AGATCGGAAGAGCACACGTCTGAACTCCAGTCA OR MaskAdapterRead2, AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT |
(Sample Sheet) AdapterRead1, AGATCGGAAGAGCACACGTCTGAACTCCAGTCA AND AdapterRead2, AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT AND AdapterBehavior, mask |
| Designate the adapter sequences for Read 1 and Read 2 and specify the behavior as trim. Also specify 0.5 as the adapter stringency. | (Sample Sheet) Adapter, AGATCGGAAGAGCACACGTCTGAACTCCAGTCA OR TrimAdapter, AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (Command Line) --adapter-stringency 0.5 |
AdapterRead1, AGATCGGAAGAGCACACGTCTGAACTCCAGTCA AND AdapterRead2, AGATCGGAAGAGCACACGTCTGAACTCCAGTCA(Sample Sheet) AND AdapterStringency, 0.5 |
| Behavior | Obsolete bcl2fastq/bcl2fastq2 Setting | New BCL Convert Setting |
|---|---|---|
| Trim the first 7 bases and last 6 bases of Read 1 for a 151 x 8 x 8 x 151 run. | (Sample Sheet) Read1StartFromCycle, 8 Read1EndWithCycle, 145 |
(Sample Sheet) N7Y137N6;I8;I8;Y151 |
| Behavior | Obsolete bcl2fastq/bcl2fastq2 Setting | New BCL Convert Setting |
|---|---|---|
| Designate the first 8 cycles of Read 1 and Read 2 as UMIs and trim the trailing base for a 151 x 8 x 8 x 151 run. | (Sample Sheet) Read1UMIStartFromCycle, 1 Read1UMILength, 8 Read1StartFromCycle, 10 Read2UMIStartFromCycle, 1 Read2UMILength, 8 Read2StartFromCycle, 10 |
(Sample Sheet) U8N1Y142;I8;I8;U8N1Y142 |
| Behavior | Obsolete bcl2fastq/bcl2fastq2 Setting | New BCL Convert Setting |
|---|---|---|
| Allow 1 mismatch in the i7 index sequence and 1 mismatch i5 index sequence. | --barcode-mismatches 1 OR --barcode-mismatches 1,1 |
BarcodeMismatchesIndex1, 1 AND BarcodeMismatchesIndex2, 1 |
| Allow 2 mismatches in the i7 index sequence and 2 mismatches in the i5 index sequence. | --barcode-mismatches 2 OR --barcode-mismatches 2,2 |
BarcodeMismatchesIndex1, 2 AND BarcodeMismatchesIndex2, 2 |
| Behavior | Obsolete bcl2fastq/bcl2fastq2 Setting | New BCL Convert Setting |
|---|---|---|
| Allow 1 mismatch in the i7 index sequence and 1 mismatch i5 index sequence. | --barcode-mismatches 1 OR --barcode-mismatches 1,1 |
BarcodeMismatchesIndex1, 1 AND BarcodeMismatchesIndex2, 1 |
| Allow 2 mismatches in the i7 index sequence and 2 mismatches in the i5 index sequence. | --barcode-mismatches 2 OR --barcode-mismatches 2,2 |
BarcodeMismatchesIndex1, 2 AND BarcodeMismatchesIndex2, 2 |
| Behavior | Obsolete bcl2fastq/bcl2fastq2 Setting | New BCL Convert Setting |
|---|---|---|
| Output corresponding fastq files to specific subdirectories. | (Sample Sheet) – [Data] section Sample_Project |
(Sample Sheet) – [Data] or [BCLConvert_Data] section Sample_Project |