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