Input Data

To run this pipeline, you will need to prepare the following data:

• sequencing data: FASTQ files in compressed (.gz) format. You should create a repository that contains your sequencing data because the data headers may need to be modified to have the correct format (e.g., 2:N:0 for UMI sequence). To create your data repository it, follow these commands:

mkdir [repository_name]
mkdir dataset

Now, you need to copie all these data in the repository_name that you created. To do that, follow thees commands:

cp path_to_the_data_file path_to_the_repository_destination
cp /work2/project/gafl/Data/Solanaceae/Solanum_lycopersicum/DNA/SPET/Invite/raw/DBC_AAOQOSDI_1_HVWC7DRXY.DUAL693_clean.fastq.gz /home/htphung/pipeline_qtlSeq/dataset 

• reference genome data: A FASTA-formatted file (.fa or .fasta) of the reference genome for the organism of interest
• sample file: A CSV-formatted file (.csv) containing sample metadata and the corresponding names of the sequencing data files. Follow these instructions to generate a properly formatted sample file.

Please make sure to have all of the required data before running the QTLseq Analysis Pipeline.