Long RNA-seq mapping

File name	Description
${input_dir}/fastq/${sample_id}.fastq	Read files (single-end sequencing)
${input_dir}/fastq/${sample_id}_1.fastq, ${input_dir}/fastq/${sample_id}_2.fastq	Read files (paired-end sequencing)
${input_dir}/sample_ids.txt	A text file with one sample ID per line.
${input_dir}/sample_classes.txt	A tab-deliminated file (with header) with two columns: sample_id, label (optional)
${input_dir}/batch_info.txt	A comma-deliminated file (with header) with at least two columns: sample_id, batch1, batch2, ... (optional)
${input_dir}/compare_groups.yaml	A YAML file defining positive and negative classes. (optional)
${config_dir}/${dataset}.yaml	A YAML file for configuration parameters for the dataset

Example config file: config/long_pe_example.yaml

Quality control (before adapter removal)

exseek.py quality_control -d ${dataset}

Remove adapter

exseek.py cutadapt -d ${dataset}

Start with clean reads

mkdir -p ${output_dir}/cutadapt
ln -f -s ${fastq_dir}/*.fastq.gz ${output_dir}/cutadapt

Quality control (after adapter removal)

exseek.py quality_control_clean -d ${dataset}

Rename fastq files

exseek.py rename_fastq -d ${dataset}

Mapping

exseek.py mapping -d ${dataset}

Count matrix

exseek.py count_matrix -d ${dataset}