MiSeq (Software Control Version 2.6)

File Structure

The file structure for a miseq run should be correct by default, but if you are having problems uploading, please verify your file structure is correct.

.
├── CompletedJobInfo.xml
├── Data
│   └── Intensities
│       └── BaseCalls
│           ├── sample1_S1_L001_R1_001.fastq.gz
│           ├── sample1_S1_L001_R2_001.fastq.gz
│           ├── sample2_S1_L001_R1_001.fastq.gz
│           ├── sample2_S1_L001_R2_001.fastq.gz
│           ├── sample3_S1_L001_R1_001.fastq.gz
│           └── sample3_S1_L001_R2_001.fastq.gz
└── SampleSheet.csv

Example files can be found: /example_sample_sheets/miseq_run/

Preparing your miseq sample sheet

Before using the uploader, you must prepare your sequencing run with IRIDA-specific project IDs. You can either enter the project IDs when you're creating your sample sheet using the Illumina Experiment Manager or after creating the sample sheet by editing SampleSheet.csv with Microsoft Excel or Windows Notepad.

An example, completed SampleSheet.csv with the Sample_Project column filled in looks like:

[Header]
IEMFileVersion,4
Investigator Name,Investigator 1
Experiment Name,Experiment
Date,2015-05-14
Workflow,GenerateFASTQ
Application,FASTQ Only
Assay,Nextera XT
Description,
Chemistry,Amplicon

[Reads]
251
251

[Settings]
ReverseComplement,0
Adapter,ATCGATCGATCG

[Data]
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
sample1,,plate1,A01,N801,ATCGAAA,S801,ATCGAAA,1,
sample2,,plate1,A01,N801,ATCGAAA,S801,ATCGAAA,1,
sample3,,plate1,A01,N801,ATCGAAA,S801,ATCGAAA,1,