Directory Upload
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: /examples/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
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,