bcl to fastq Conversion

Question

[BioRyder]

Hello,

I am trying to convert bcl to fastq by bcl2fastq v2.16.0.10. my Index length is 6. I have used --use-bases-mask option as follows:

--use-bases-mask Y*,I6n,y*

Is it correct base mask option .. ?

Answer 1

[harold.smith.tarheel]

If it's standard Illumina-type single indexing of paired-end reads, then yes. But, unless you have a reason to include the final low-quality base, it's not necessary to specify the mask. Default behavior is Y*n,I6n,Y*n (at least, it is for v1).

[BioRyder]

Hello,

I used the following -m=Y*,I8n*,Y* base mask option in bcl2fastq 1.8.4 version in got the out put.But When I am using same in bcl2fastq v2.16.0.10, --use-bases-mask Y*,I8n*,Y*,showing the error that

std::exception::what: UseBasesMask formatting error. Mask size does not match number of cycles in RunInfo.xml. RunInfo.xml cycles: 9 Base mask: 'iiiiiiiin*'

Index length is : 8

[harold.smith.tarheel]

If the index read is only 8bp long, then you can't use a 9bp mask like I8n; just use I8. If the index is 9bp long, then the trailing '*' is the problem; use I8n.