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Old 03-09-2012, 04:07 AM   #1
nxtgenkid10
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Default bowtie paired end

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
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Old 03-09-2012, 06:23 AM   #2
dpryan
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Quote:
Originally Posted by nxtgenkid10 View Post
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?
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Old 03-10-2012, 02:29 AM   #3
yumtaoist
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dpryan is right, the arguments are case sensitive
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Old 04-10-2012, 09:49 PM   #4
nxtgenkid10
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thanks i will try
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