NextSeq2000
The Software on the NextSeq2000 does not allow for automatic generation of a SampleSheet that includes a project column, so create a copy of the sample sheet called UploadList.csv and add the Sample_Project
column ourselves.
If you would like to use this parser you will also need to create this new file and Sample_Project
column.
File Structure
Please verify your file structure is correct.
.
├── CopyComplete.txt
├── UploadList.csv
├── Analysis
│ └── 1
│ └── Data
│ └── 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
Example files can be found: /examples/nextseq2k_run/
Preparing your nextseq2000 upload list
Before using the uploader, you must prepare your sequencing run with IRIDA-specific project IDs.
Copy and rename the CSV file made by the software to UploadList.csv
(It will have a name something like NGS-1001 BCLconvert.csv
)
Then add the Sample_Project
column to the [BCLConvert_Data]
table.
An example completed UploadList.csv
with the Sample_Project
column filled in looks like:
[Header]
FileFormatVersion,2
Run Name,NGS1001
InstrumentPlatform,NextSeq1k2k
InstrumentType,NextSeq2000
[Reads]
Read1Cycles,101
Read2Cycles,101
Index1Cycles,8
Index2Cycles,8
[BCLConvert_Settings]
SoftwareVersion,3.5.8
AdapterRead1,CTGTCTTCTCTCTC
AdapterRead2,CGTCTCTCTCTCTC
[BCLConvert_Data]
Sample_ID,Index,Index2,Sample_Project
sample1,ATCGAAA,ATCGAAA,1
sample2,ATCGAAA,ATCGAAA,1
sample3,ATCGAAA,ATCGAAA,2