bcl2fastq-v2 samplesheet format for dual index run

Question

[jacobnix]

Hello everybody,

We are using bcl2fastq-v2 for nextseq runs without problems (one index runs). Does anyone know which is the samplesheet format for illumina nextseq dual index run?

I have been experimenting with different columns but does not work ,the manual lists 2 columns index, index2, but I have not seen any tutorial to be used

my csv data section is:

[Data]
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,SampleProject,Description
1,LS1VP2SS01-701-501,LS1VP2SS01-701-501,,,,TAAGGCGA-GCGATCTA,HLTFJBGXX,
1,LS1VP2SS03-701-503,LS1VP2SS03-701-503,,,,TAAGGCGA-AGAGGATA,HLTFJBGXX,
1,LS1VP2SS04-702-504,LS1VP2SS04-702-504,,,,CGTACTAG-TCTACTCT,HLTFJBGXX,
1,LS1VP2SS05-702-505,LS1VP2SS05-702-505,,,,CGTACTAG-CTCCTTAC,HLTFJBGXX,
1,LS1VP2SS06-702-506,LS1VP2SS06-702-506,,,,CGTACTAG-TATGCAGT,HLTFJBGXX,
1,LS1VP2SS07-703-507,LS1VP2SS07-703-507,,,,AGGCAGAA-TACTCCTT,HLTFJBGXX,

Which columns are strictly necessary?

Thanks in advance

Jacob

Answer 1

[GenoMax]

Download Illumina Experiment Manager software (note: this is Windows only, v.1.11 is the latest) and create a test SampleSheet. This SampleSheet is guaranteed to work with Illumina software.

Answer 2

[BioRyder]

Hello jacobnix,

For dual index, Sample sheet format should be in below format .While doing bcltofastq conversion you should use the base mask as it like: --use-bases-mask Y*,I*,I*,Y*. (Note: each I for Index 1 & Index 2 respectively)

Sample sheet Format:

[Data]
Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,index2,SampleProject,Description