File Structure
The file structure for a NextSeq run will need bcl2fastq
run first to produce usable fastq files.
The generated structure should automatically work with the parser.
WARNING! If using --batch
upload with an auto-upload script, incomplete fastq files could be uploaded if bcl2fastq
has not finished when the upload begins.
If you are having problems uploading, please verify your file structure is correct.
<In this example, the run is has sequence data for project 22 and project 23
.
├── CompletedJobInfo.xml
├── Data
│ └── Intensities
│ └── BaseCalls
│ ├── 67
│ │ ├── SA20121712_S2_R1_001.fastq.gz
│ │ ├── SA20121712_S2_R2_001.fastq.gz
│ └── 68
│ ├── SA20121716_S2_R1_001.fastq.gz
│ └── SA20121716_S2_R2_001.fastq.gz
├── RTAComplete.txt
└── <other files>
Example files can be found: /example_sample_sheets/nextseq_run/
Example NextSeq sample sheet
[Header]
IEMFileVersion,5
Investigator Name,Ikari Yui
Experiment Name,NGS-Adam
Date,2000-09-13
Workflow,GenerateFASTQ
Application,NextSeq FASTQ Only
Instrument Type,NextSeq/MiniSeq
Assay,Nextera XT
Index Adapters,"Nextera XT v2 Index Kit A"
Description,Contact Experiment
Chemistry,Amplicon
[Reads]
151
151
[Settings]
Adapter,CTGTCTCTTATACACATCT
[Data]
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
SA20121716,SA20121716,NGS-001 Plate FNC-7,A01,N701,TAAGGCGA,S502,ATAGAGAG,1094,Code Blue
SA20121712,SA20121712,NGS-001 Plate FNC-7,A02,N702,CGTACTAG,S502,ATAGAGAG,1094,Code Blue