You will need to create a design file with information about the samples in your experiment before running the pipeline. It has to be a comma-separated file with 5 columns, and a header row as shown in the example below:
sample,replicate,run,fastq_1,fastq_2
control,1,1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
control,2,1,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz
treatment,1,1,AEG588A3_S5_L003_R1_001.fastq.gz,AEG588A3_S5_L003_R2_001.fastq.gz
treatment,2,1,AEG588A4_S3_L002_R1_001.fastq.gz,AEG588A4_S3_L002_R2_001.fastq.gz
treatment,2,2,AEG588A5_S4_L002_R1_001.fastq.gz,AEG588A5_S4_L002_R2_001.fastq.gz| Column | Description |
|---|---|
sample |
Group identifier for sample. |
replicate |
Integer representing replicate number. |
run |
Integer representing the number of times the same library has been sequenced. This will be used later for merging at the replicate-level. |
fastq_1 |
Full path to FastQ file for read 1. File has to be zipped and have the extension ".fastq.gz". |
fastq_2 |
Full path to FastQ file for read 2. File has to be zipped and have the extension ".fastq.gz". |