> Error in tophat:
> 
> [2013-02-13 02:02:43] Beginning TopHat run (v2.0.7)
> -----------------------------------------------
> [2013-02-13 02:02:43] Checking for Bowtie
>                 Bowtie version:        2.0.6.0
> [2013-02-13 02:02:43] Checking for Samtools
>               Samtools version:        0.1.18.0
> [2013-02-13 02:02:43] Checking for Bowtie index files
> Error: Could not find Bowtie 2 index files 
> (/data/bowtie2-2.0.6/hg19/Homo_sapiens/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/.*.bt2)
> The tool produced the following additional output:
> TopHat v2.0.7
> tophat2 -p 4  
> /data/bowtie2-2.0.6/hg19/Homo_sapiens/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/
>  /opt/galaxyprod/galaxy-dist/database/files/000/dataset_197.dat
> I have these files under the Index directory:
> genome.1.bt2  genome.2.bt2  genome.3.bt2  genome.4.bt2  genome.fa  
> genome.rev.1.bt2  genome.rev.2.bt2  tophat_out

Your path to your indices should like like this:

/data/bowtie2-2.0.6/hg19/Homo_sapiens/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome

Best,
J.

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