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<div><br>
</div><div>with the files:</div><div><br></div><div><div>genome.1.bt2  genome.2.bt2  genome.3.bt2  genome.4.bt2  genome.rev.1.bt2  genome.rev.2.bt2</div><div><br></div><div><br></div><div>While adding the reference gnome, I need to edit bowtie2_indices.loc</div>
</div><div><br></div><div>Shall I replace:</div><div><br></div><div><div>/orig/path/hg19        hg19    hg19                    /depot/data2/galaxy/bowtie2/hg19/hg19</div></div><div><br></div><div>with</div><div><br></div>
<div><div>hg19   hg19    hg19   Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index</div></div><div><br></div><div><br></div><div>Thanks,</div><div><br></div><div>Sachit</div>