I had paired end illumina reads of a bacterial genome and i have the reference so i m trying to use bowtie to align the same . so first i made the index of reference and used the following commands
bowtie2 /Reference/genome -1 /DATA/Read1.fastq -2 /DATA/Read2.fastq -S phix.sam
But i couldnt give the -n and -l command
Y is it so ? and how could i give them
bowtie2 /Reference/genome -1 /DATA/Read1.fastq -2 /DATA/Read2.fastq -S phix.sam
But i couldnt give the -n and -l command
Y is it so ? and how could i give them
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