Question: Tophat error on using NONCODE database gtf file.
0
gravatar for cfarmeri
5.0 years ago by
cfarmeri160
Japan
cfarmeri160 wrote:

Dear all,

I am a beginner with Tophat and I am trying to align RNA seq reads to the mouse genome.

 

When I was mapping my fastq file to the reference genome(GRCm38) by tophat(v2.0.9),

I use NONCODEv4_mouse_lncRNA.gtf from NONCODE.v4 as an annotation gtf file.

 

The commad is following:

tophat -G NONCODEv4_mouse_lncRNA.gtf <index> <reads.fastq>

 

I got the following in tophat log:

----------

[FAILED] Error: gtf_to_fasta returned an error.

----------

Please tell me how to solve this proble.

thanks.

 

rna-seq • 1.6k views
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by cfarmeri160

This question is a possible duplicate of this one: Tophat Error: Gtf To Fasta Returned An Error
Try the answers proposed in that question and come back if you're still in troubles :).

ADD REPLYlink written 5.0 years ago by iraun3.7k
0
gravatar for cfarmeri
5.0 years ago by
cfarmeri160
Japan
cfarmeri160 wrote:

Thank you for your advice.
I tried the solution of that question:Tophat Error: Gtf To Fasta Returned An Error

But I received another error from tophat.

That is following:

-------

Error: Couldn't build bowtie index with err = 1

------

The FASTA file from NONCODE gtf file generated by gtf_to_fata(in tophat) was empty.

(The NONCODE gtf file is from http://www.noncode.org/download.php)

So I'm sure that this error also occured at gtf_to_fasta in tophat.

Please tell me what I sould do.

Thanks.

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by cfarmeri160
0
gravatar for Manvendra Singh
5.0 years ago by
Manvendra Singh2.1k
Berlin, Germany
Manvendra Singh2.1k wrote:

give multithread options, -p

may be your system doesn't have enough memory to run tophat

ADD COMMENTlink written 5.0 years ago by Manvendra Singh2.1k
0
gravatar for cfarmeri
5.0 years ago by
cfarmeri160
Japan
cfarmeri160 wrote:

I gave multiread options -p 3.

So the memory may  be enough to run tophat.....

ADD COMMENTlink written 5.0 years ago by cfarmeri160
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