#Sample_name fastq_file reference alignment.paired_end application options sample_1 /data/FC01/demultiplexed/sample_1/s_sample_1.fastq /data/Genomes/Bowtie/hg19 0 chipseq sample_2 /data/FC01/demultiplexed/sample_2/s_sample_2.fastq /data/Genomes/Bowtie/hg19 0 chipseq