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Old 12-12-2011, 08:17 AM   #1
rebrendi
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Default TopHat Error: Could not find Bowtie index files /bowtie-0.12.5/indexes/.

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:

Quote:
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!
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Old 12-12-2011, 08:40 AM   #2
NM_010117
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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:
Code:
tophat -r 20 /bowtie-0.12.5/indexes/genome_file_name /data_with_reads/sequence.txt
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Old 12-12-2011, 08:58 AM   #3
rebrendi
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Quote:
Originally Posted by NM_010117 View Post
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:
Code:
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
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Old 12-12-2011, 09:24 AM   #4
NM_010117
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You actually won't specify a file, but rather the base file name. So, in this case your command would be:
Code:
tophat -r 20 /bowtie-0.12.5/indexes/hg18 /data_with_reads/read_1.fastq /data_with_reads/read_2.fastq
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Old 12-12-2011, 09:29 AM   #5
dpryan
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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:
Code:
export BOWTIE_INDEXES=/bowtie-0.12.5/indexes
then you should be able to run your alignments:
Code:
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.
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Old 12-12-2011, 09:47 AM   #6
rebrendi
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NM_010117, dpryan,
Thank you, this helped!
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Old 08-23-2012, 04:19 PM   #7
lixiaojin
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Thank you, NM 010117. Your answer to rebrendi helped me.
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Old 05-12-2014, 12:52 PM   #8
jwhite
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Quote:
Originally Posted by dpryan View Post
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:
Code:
export BOWTIE_INDEXES=/bowtie-0.12.5/indexes
then you should be able to run your alignments:
Code:
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
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Old 05-12-2014, 01:03 PM   #9
dpryan
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You can just specify the path along with the base, so "/I'm/some/random/path/some_base" will work.
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Old 05-12-2014, 02:03 PM   #10
GenoMax
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*All* index files with that specific base name have to be in the path (directory) that Devon mentions above.
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Old 06-22-2016, 08:50 AM   #11
luana
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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!
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Old 06-22-2016, 09:55 AM   #12
dpryan
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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.
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