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
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to