Bowtie2: Why won't it recognize my index files?

Question

[Kristin Muench]

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?

[m.ghanatbari]

Oh I found my mistake, the command should be like this:

$ tophat2 UCSD_hg19/Bowtie2Index/hg19 UCSD_hg19/SRR1198830.fastq
---------------------------------^^^^

[m.ghanatbari]

$ tophat2 UCSD_hg19/Bowtie2Index/ UCSD_hg19/SRR1198830.fastq

TopHat run (v2.0.11)
 Bowtie version:        2.1.0.0
Samtools version:        0.1.18.0
[2015-10-17 20:40:58] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (UCSD_hg19/Bowtie2Index/.*.bt2)

Actually, I have index files in Bowtie2Index folder, but still shows me this error. I couldn't fix it. I am suspicious to the TopHat version, but I am just a user in TACC cloud, so I don't have admin privileges to update the version. Is the any suggestion?

Answer 1

[iraun]

If you see tophat help:

Usage:
    tophat [options] <bowtie_index>

You are trying to put the bowtie index with -G parameter, and -G is for specifying an annotation file.

-G/--GTF       <filename>  (GTF/GFF with known transcripts)

[Kristin Muench]

Aha, thank you so much! I misunderstood the -G option. It seems to work fine now!