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
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