base mask option in bcl to fastq conversion

Question

[BioRyder]

Hello,

I used the -m=Y*,I8n*,Y* base mask option in bcl2fastq 1.8.4 version in got the output. 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

[Devon Ryan]

Try --use-bases-mask Y*,I8n,Y*, it'll probably work assuming you actually had a 9 base index.

[BioRyder]

Thanks it is working fine with --use-bases-mask Y*,I8n,Y*.

One more question: I have total 8 lane and lane 1 & two are with no index and others are having index with length 8. I this situation will it work --use-bases-mask Y*,I8n,Y* option.? When I tested with this option some of lane are coming with zero size data.

[GenoMax]

You may have to run this two times. Once to get the six that have the index. Other time to get the two lanes that do not have an index (--use-bases-mask Y*,n*,Y*) with just those two samples in the samplesheet.

[harold.smith.tarheel]

Leave the index field empty in the sample sheet for lanes one and two (this works for v1 software).

[Devon Ryan]

Normally each lane gets an undetermined fastq file, in which case the lanes with no index should have all of their data placed there. That's how the V2 software seems to work for me, though I've never needed to mix indexed and unindexed lanes.