bowtei for multiple pair end library

[jjjscuedu]

Dear all,

I want to use bowtie to generate the sam file for my pair end file.

However, I have several pair end file like this:

lib1_1.fq lib1_2.fq
lib2_1.fq lib2_2.fq
lib3_1.fq lib3_2.fq

Do anyone know how can I use bowtie for multiple library?

Thx.

Jingjing

[dpryan]

Just run bowtie once for each library. You'll want to set the meta-information differently for each library anyway.