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:
When uploading paired end reads, your file names must indicate forward/reverse.
Use the same name between files, with the difference of including
r, as shown above.
Preparing your sample list file
Before using the uploader, you must create a
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
Alternatively, full file paths can be used when specifying files:
[Data] Sample_Name,Project_ID,File_Forward,File_Reverse my-sample-1,5,/home/user/my_file_dir/directory_run/file_1.fastq.gz, my-sample-2,5,/home/user/my_file_dir/directory_run/samp_F.fastq.gz,