Tophat can't find Bowtie index files

[colinmolter]

transcriptome_index

[QUOTE=billstevens;75627]Hey guys, I'm having trouble getting my Tophat run to start. Here is my code:

tophat -p 4 -G hg19_knowngene2.gtf \ --transcriptome-index=transcriptome_data/known \ hg19 Luxs-11-23_ACTTGA_L005_R1_001.fastq.gz,Luxs-11-... ,Luxs-11-23_ACTTGA_L005_R2_007.fastq.gz > output.txt 2> errors.txt 0> input.txt]

Hi, I never used the transcriptome_index, but what I understood about it is that it should replace the '-G hg19' option at the second pass.
In fact, i was wondering if I am all the time working with hg19, if I could create these index once and then use them by not mentioning the -G option.
Does anyone has good clues about how to use it?

thanks
colin

[Dario1984]

You have a space before the escape character. It's only supposed to be after it.

[billstevens]

Hey guys, I'm having trouble getting my Tophat run to start. Here is my code:

tophat -p 4 -G hg19_knowngene2.gtf \ --transcriptome-index=transcriptome_data/known \ hg19 Luxs-11-23_ACTTGA_L005_R1_001.fastq.gz,Luxs-11-23_ACTTGA_L005_R1_002.fastq.gz,Luxs-11-23_ACTTGA_L005_R1_003.fastq.gz,Luxs-11-23_ACTTGA_L005_R1_004.fastq.gz,Luxs-11-23_ACTTGA_L005_R1_005.fastq.gz,Luxs-11-23_ACTTGA_L005_R1_006.fastq.gz,Luxs-11-23_ACTTGA_L005_R1_007.fastq.gz Luxs-11-23_ACTTGA_L005_R2_001.fastq.gz,Luxs-11-23_ACTTGA_L005_R2_002.fastq.gz,Luxs-11-23_ACTTGA_L005_R2_003.fastq.gz,Luxs-11-23_ACTTGA_L005_R2_004.fastq.gz,Luxs-11-23_ACTTGA_L005_R2_005.fastq.gz,Luxs-11-23_ACTTGA_L005_R2_006.fastq.gz,Luxs-11-23_ACTTGA_L005_R2_007.fastq.gz > output.txt 2> errors.txt 0> input.txt

I have the six hg19.ebwt index files in the directory.

I keep getting this error:
Could not find Bowtie index files --transcriptome-index=transcriptome_data/known.

What do you guys think?

[cedance]

Hi Colin,
I have

<basename>.1.bt2
<basename>.2.bt2
<basename>.3.bt2
<basename>.4.bt2
<basename>.rev.1.bt2
<basename>.rev.2.bt2

Maybe your indexing was not complete?

[colinmolter]

I have the same error. Though the bowtie2 index are there:

tophat2 /path/Bowtie2Index/hg19 mysample.fastq

-->
[2012-05-22 22:49:13] Beginning TopHat run (v2.0.0)
-----------------------------------------------
[2012-05-22 22:49:13] Checking for Bowtie
Bowtie version: 2.0.0.6
[2012-05-22 22:49:13] Checking for Samtools
Samtools version: 0.1.18.0
[2012-05-22 22:49:13] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files (/path/Bowtie2Index/hg19.*.bt2)

but:
ls -lh /path/Bowtie2Index/hg19.*

-rw-r--r-- 1 916M /path/Bowtie2Index/hg19.1.bt2
-rw-r--r-- 1 684M /path/Bowtie2Index/hg19.2.bt2

do i miss something?

thanks
colin

[JohnGa]

Thanks for help

Very helpful. Thanks a lot.

[cedance]

Or build one from your reference genome

[Dario1984]

You should get new indexes from the Bowtie2 website.

[JohnGa]

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)
-----------------------------------------------
[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)