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/hg19hg19hg19
> /depot/data2/galaxy/bowtie2/hg19/hg19
>
> with
>
> hg19 hg19hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index
>
>
> Thanks,
>
> Sachit
>
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