BCL Convert Compatible Products

Compatibility Between BCL Convert and bcl2fastq2

Adapter Behavior and Specifications
Behavior Obsolete Sample Sheet Settings New Sample Sheet Settings
Designate the adapter sequences for Read 1 and Read 2 and specify the behavior as trim.

Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

OR

TrimAdapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

AdapterRead1,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

AND

AdapterRead2,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

Designate the same adapter sequence for Read 1 and Read 2 and specify the behavior as mask. MaskAdapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

AdapterRead1,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

AND

AdapterRead2,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

AND

AdapterBehavior,mask

Designate the adapter sequences for Read 1 and Read 2 and specify the behavior as mask.

MaskAdapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

OR

MaskAdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

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.

Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

OR

TrimAdapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
(command line) --adapter-stringency 0.5

AdapterRead1,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

AND

AdapterRead2,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA

AND

AdapterStringency, 0.5

Read Trimming
Behavior Obsolete Sample Sheet Settings New Sample Sheet Settings
Trim the first 7 bases and last 6 bases of Read 1 for a 151 x 8 x 8 x 151 run.

Read1StartFromCycle,8

Read1EndWithCycle,145

OverrideCycles,N7Y137N6;I8;I8;Y151
UMI Specification
Behavior Obsolete Sample Sheet Settings New Sample Sheet Settings

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.

Read1UMIStartFromCycle,1

Read1UMILength,8

Read1StartFromCycle,10

Read2UMIStartFromCycle,1

Read2UMILength,6

Read2StartFromCycle,9

OverrideCycles,U8N1Y142;I8;I8;U6N2Y142

Barcode Mismatches
Behavior Obsolete Command Line Settings New Sample Sheet Settings
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

Masking of Trimmed Reads
Behavior Obsolete Command Line Settings New Sample Sheet Settings
Make sure that all trimmed reads are at least 10 base pairs long after adapter trimming by appending Ns to any read shorter than 10 base pairs.

--minimium-trimmed-read-length 10

MinimumTrimmedReadLength, 10

Make sure that all trimmed reads below 5 base pairs long are masked with Ns.

--mask-short-adapter-reads, 5

MaskShortReads, 5