File Structure

To upload using the directory parser, Organize your files according to the following

.
├── file_1.fastq.gz
├── file_2.fastq.gz
├── samp_F.fastq.gz
├── samp_R.fastq.gz
├── germ_f.fastq.gz
├── germ_r.fastq.gz
└── SampleList.csv

Example files can be found: /example_sample_sheets/directory_run/

File Names

When uploading paired end reads, your file names must indicate forward/reverse.

Use the same name between files, with the difference of including 1 / 2, F / R, f / r, as shown above.

Preparing your sample list file

Before using the uploader, you must create a SampleList.csv file.

It must contain the following fields

Sample_Name : This is what the sample will be identified as on IRIDA after upload.

Project_ID: The IRIDA project the sample will be uploaded to.

File_Forward: Always needed, the forward read file.

File_Reverse: Needed for paired end reads, the reverse read file.

An example, completed SampleList.csv with all the columns filled in looks like:

[Data]
Sample_Name,Project_ID,File_Forward,File_Reverse
my-sample-1,75,file_1.fastq.gz,file_2.fastq.gz
my-sample-2,75,samp_F.fastq.gz,samp_R.fastq.gz
my-sample-3,76,germ_f.fastq.gz,germ_r.fastq.gz

Another example, but with only single end reads:

[Data]
Sample_Name,Project_ID,File_Forward,File_Reverse
my-sample-1,75,file_1.fastq.gz
my-sample-2,75,samp_F.fastq.gz
my-sample-3,76,germ_f.fastq.gz