bowtie paired end

[nxtgenkid10]

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

[dpryan]

But i couldnt give the -n and -l command
Y is it so ? and how could i give them

Aren't they -N and -L in bowtie2?

[yumtaoist]

dpryan is right, the arguments are case sensitive

[nxtgenkid10]

thanks i will try