Also, do I have make all the reference files executable? <br><br><div class="gmail_quote">On Wed, Feb 13, 2013 at 6:39 AM, Sachit Adhikari <span dir="ltr">&lt;<a href="mailto:sachit.technerves@gmail.com" target="_blank">sachit.technerves@gmail.com</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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>
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</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>
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