TopHat Error: Could not find Bowtie index files /bowtie-0.12.5/indexes/.

[rebrendi]

Hello all,

I am using TopHat for the first time and it does not find my bowtie indexes. I have an old version of Bowtie installed; all the indexes that I need are there (I used it before, no problem). When I run TopHat, it gives the following error:

tophat -r 20 /bowtie-0.12.5/indexes /data_with_reads/sequence.txt

Error: Could not find Bowtie index files /bowtie-0.12.5/indexes/.*

This directory actually contains all the bowtie indexes (all genomes that I used before). Should I reformat/rename/reorganize this old bowtie directory somehow?

Any help?
Thanks!

[NM_010117]

The problem is that you need to specify in the command the name of the bowtie index in addition to the folder.

So, something like this instead:

tophat -r 20 /bowtie-0.12.5/indexes/genome_file_name /data_with_reads/sequence.txt

[rebrendi]

The problem is that you need to specify in the command the name of the bowtie index in addition to the folder.

So, something like this instead:

tophat -r 20 /bowtie-0.12.5/indexes/genome_file_name /data_with_reads/sequence.txt

Thank you for the suggestion. Do you know which of the following files in the indexes directory should be specified?

hg18.1.ebwt
hg18.2.ebwt
hg18.3.ebwt
hg18.4.ebwt
hg18.rev.2.ebwt
hg18.rev.1.ebwt

[NM_010117]

You actually won't specify a file, but rather the base file name. So, in this case your command would be:

tophat -r 20 /bowtie-0.12.5/indexes/hg18 /data_with_reads/read_1.fastq /data_with_reads/read_2.fastq

[dpryan]

Just "hg18", without the quotes. From the TopHat manual, you just specify the "basename", which I recall being hg18, or mm9, or whatever you're using. You can then set the PATH in the BOWTIE_INDEXES environment variable. If you're using bash:

export BOWTIE_INDEXES=/bowtie-0.12.5/indexes

then you should be able to run your alignments:

tophat -r 20 hg18 /path/to/reads.fastq

You can also set the BOWTIE_INDEXES variable in your .bashrc (or equivalent) if you'll be doing this often.

[rebrendi]

NM_010117, dpryan,
Thank you, this helped!

[lixiaojin]

Thank you, NM 010117. Your answer to rebrendi helped me.

[jwhite]

Just "hg18", without the quotes. From the TopHat manual, you just specify the "basename", which I recall being hg18, or mm9, or whatever you're using. You can then set the PATH in the BOWTIE_INDEXES environment variable. If you're using bash:

export BOWTIE_INDEXES=/bowtie-0.12.5/indexes

then you should be able to run your alignments:

tophat -r 20 hg18 /path/to/reads.fastq

You can also set the BOWTIE_INDEXES variable in your .bashrc (or equivalent) if you'll be doing this often.

Hi,

Is there a command line option to specify the bowtie index path? Our indexes are stored in a different location from bowtie and have different names from the ususal. Using the methods you listed tophat --fusion... still cannot find its indexes --no matter what path and filename I list.

Joe White

[dpryan]

You can just specify the path along with the base, so "/I'm/some/random/path/some_base" will work.

[GenoMax]

*All* index files with that specific base name have to be in the path (directory) that Devon mentions above.

[luana]

tophat --color --quals fr-secondstrand Bowtie-directory/BOWTIE/ebwt_base -o NGR1_NGR2_1_thout genome NFN_run6_Transcriptoma_29102013_bcSample1_F3_NGR1.csfasta NFN_run6_Transcriptoma_29102013_bcSample1_F3_NGR2.csfasta NFN_run6_Transcriptoma_29102013_bcSample1_F3_QV_NGR1.qual NFN_run6_Transcriptoma_29102013_bcSample1_F3_QV_NGR2.qual

Beginning TopHat run (v2.1.0)
Checking for Bowtie
Bowtie version: 1.1.1.0
[2016-06-22 13:23:45] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie index files (fr-secondstrand.*.ebwt)

the bowtie don't find the file index!

[dpryan]

Look at the actual error message. Sure, it says it can't find them, but look at the names of what you're telling it your indexes are called. Hint: you can't just randomly put "fr-secondstrand" anywhere in the command.