I am attempting to use TopHat2 (and, consequently, Bowtie2) on a computer cluster. Since it's on someone else's cluster, I did not do the installation of Bowtie, nor do I have control of the bowtie2-index.loc files.

I have a directory, .../Assemblies/hg19/, containing these files (the index files/reference files for Bowtie2):

hg19.1.bt2
hg19.3.bt2
hg19.2.bt2
hg19.4.bt2
hg19.rev.1.bt2
hg19.rev.2.bt2
hg19.zip
make_hg19.sh

I point to these index files using tophat2 -G [indexFileDirectory]. However, I cannot get tophat2 to register the files appropriately.

For instance, if I write [indexFileDirectory] as:

.../Assemblies/hg19/hg19

(The ... represents a directory path), then I get this error:

Error: cannot find transcript file .../Assemblies/hg19/hg19

Here's a table of corresponding index file location and errors

[indexfileDirectory]      Error
…/Assemblies/hg19/        Error: is a directory
…/Assemblies/hg19/hg19    Error: cannot find transcript file .../Assemblies/hg19/hg19
…/Assemblies/hg19/*       Error: Could not find Bowtie 2 index files (.../Assemblies/hg19/hg19.2.bt2.*.bt2)
…/Assemblies/hg19/*hg19*  Error: Could not find Bowtie 2 index files (.../Assemblies/hg19/hg19.2.bt2.*.bt2)
…/Assemblies/hg19/hg19*   Error: Could not find Bowtie 2 index files (.../Assemblies/hg19/hg19.2.bt2.*.bt2)

My review of internet forums sounds like the second option (.../hg19/hg19) should be the one that works. I'm going nuts! Did anyone else have this problem?