Also, do I have make all the reference files executable? On Wed, Feb 13, 2013 at 6:39 AM, Sachit Adhikari < sachit.technerves@gmail.com> wrote:

I downloaded the entire directory of UCSC for the reference gnome of Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference gnome. I found a directory: Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index

with the files:

genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2 genome.rev.1.bt2 genome.rev.2.bt2

While adding the reference gnome, I need to edit bowtie2_indices.loc

Shall I replace:

/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19

with

hg19 hg19 hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index

Thanks,

Sachit