MiSeq (Software Control Version 3.1)
The file structure for a MiSeq run when making fastq files should work by default, but if you are having problems uploading, please verify your file structure is correct.
. ├── CompletedJobInfo.xml ├── Alignment_1 │ └── <DateTimeFolder> │ └── Fastq │ ├── 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 │ └── <other files> ├── SampleSheet.csv └── <other files>
Example files can be found:
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,