And when I tried running tophat alone like this: tophat -r 20 test_ref reads_1.fq reads_2.fq I get this error: [2012-12-19 06:57:07] Beginning TopHat run (v2.0.7) ----------------------------------------------- [2012-12-19 06:57:07] Checking for Bowtie Bowtie version: 2.0.2.0 [2012-12-19 06:57:07] Checking for Samtools Samtools version: 0.1.18.0 [2012-12-19 06:57:07] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (test_ref.*.bt On Wed, Dec 19, 2012 at 10:38 AM, Sachit Adhikari < sachit.technerves@gmail.com> wrote:

This is the error I am getting while running Tophat. What's causing this? I have the default hg19 index files.

Error in tophat:

[Tue Dec 18 10:08:33 2012] Beginning TopHat run (v1.3.3) ----------------------------------------------- [Tue Dec 18 10:08:33 2012] Preparing output location ./tophat_out/ [Tue Dec 18 10:08:33 2012] Checking for Bowtie index files Error: Could not find Bowtie index files /opt/galaxyprod/galaxy-dist/data/hg19/hg19,/data/bowtie2-2.0.2/hg19.*

TopHat v1.3.3 TopHat v1.3.3 tophat -p 4 /opt/galaxyprod/galaxy-dist/data/hg19/hg19,/data/bowtie2-2.0.2/hg19 /opt/galaxyprod/galaxy-dist/database/files/000/dataset_45.dat