Reference sequence files are in the folder /bigfiles/Brassica/reference_dir

One percent random read files are in the folder /bigfiles/Brassica/read_dir


Running Bowtie
  Build bowtie index file:
    /home/zhangju/App/bowtie2-2.1.0/bowtie2-build reference_fasta index_name

  Run alignment:
    /home/zhangju/App/bowtie2-2.1.0/bowtie2 -x index -U unmapped_fastq_file -S Alignment_output.sam