build fa to index $ align it resulting a sam file
Indexing a reference genome
$BT2_HOME/bowtie2-build $BT2_HOME/example/reference/lambda_virus.fa lambda_virus
the current directory will contain four new files that all start with lambda_virus and end with .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, and .rev.2.bt2.
Aligning example reads
$BT2_HOME/bowtie2 -x lambda_virus -U $BT2_HOME/example/reads/reads_1.fq -S eg1.sam
sort & index
igvtools sort eg.sam sorted_eg.sam
igvtools index sorted_eg.sam (return sam&sam.sai)
java -Xmx1g -jar ./igvtools.jar sort eg.sam sorted_eg.sam
sam to bam
samtools view -bS out.sam > out.bam
samtools sort out.bam > result
samtools index result.bam (return bam&bam.bai)
