Make you are in "interactive mode" 1) Download cassava genome from phytozome

wget ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Mesculenta/assembly/Mesculenta_147.fa.gz

2) created a directory called cassava

mkdir cassava

3) move fasta sequence in the directory

mv Mesculenta_147.fa.gz cassava/

4) uncompress using gunzip

cd cassava
gunzip Meculenta_147.fa.gz

5) Count number of scaffold in the file

grep ">" Mesculenta_147.fa | wc

6) load bowtie module

module load bowtie2

7) Create the bowtie index.

bowtie2-build Mesculenta_147.fa cassava

8) Run Bowtie using single end fastq as input. See bowtie2 for instructions on how to run it on pair-end sequences.

bowtie2 -x cassava/cassava -U test.fastq -S test.sam