Question: bcl2fastq-v2 samplesheet format for dual index run
0
gravatar for jacobnix
2.7 years ago by
jacobnix0
jacobnix0 wrote:

Hello everybody ,

we are using bcl2fastq-v2 for nextseq runs without problems (one index runs) ,

someone knows 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 ?

:S

Thanks in advance

Jacob

nextseq bcl2fastq illumina • 3.9k views
ADD COMMENTlink modified 2.7 years ago by BioRyder160 • written 2.7 years ago by jacobnix0
2
gravatar for genomax
2.7 years ago by
genomax58k
United States
genomax58k wrote:

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.

 

 

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by genomax58k
0
gravatar for BioRyder
2.7 years ago by
BioRyder160
India
BioRyder160 wrote:

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

ADD COMMENTlink written 2.7 years ago by BioRyder160
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