New to TopHat/Bowtie. I have already set PATH for bowtie2, tophat and samtools. However, when I was trying tophat using the test example from tophat website and the Nature Protocols example/procedure, the following error message was shown. I tried ln (link file), adding path-to-directory before file, and exporting path for the directory containing index files (actually in the same directory), but none of them worked. The error message asks for .bt2 index files, but all provided index files are in .ebwt format. Should I change file extension? Please advise. Thanks in advance.
[2012-05-17 14:54:46] Beginning TopHat run (v2.0.0)
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[2012-05-17 14:54:46] Checking for Bowtie
Bowtie version: 2.0.0.6
[2012-05-17 14:54:46] Checking for Samtools
Samtools version: 0.1.18.0
[2012-05-17 14:54:46] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files (test_ref.*.bt2)
[2012-05-17 14:54:46] Beginning TopHat run (v2.0.0)
-----------------------------------------------
[2012-05-17 14:54:46] Checking for Bowtie
Bowtie version: 2.0.0.6
[2012-05-17 14:54:46] Checking for Samtools
Samtools version: 0.1.18.0
[2012-05-17 14:54:46] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files (test_ref.*.bt2)
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