Question: base mask option in bcl to fastq conversion
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gravatar for BioRyder
4.6 years ago by
BioRyder170
India
BioRyder170 wrote:

Hello ,

I used the -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

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ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by BioRyder170

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

ADD REPLYlink written 4.6 years ago by Devon Ryan95k

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.

ADD REPLYlink modified 6 months ago by RamRS27k • written 4.6 years ago by BioRyder170

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.

ADD REPLYlink modified 6 months ago by RamRS27k • written 4.6 years ago by genomax84k

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

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by harold.smith.tarheel4.5k

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.

ADD REPLYlink written 4.6 years ago by Devon Ryan95k
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