Tophat error on using NONCODE database gtf file.

Question

[cfarmeri]

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 command is:

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 problem.

Thanks

[iraun]

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 :).

[cfarmeri]

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_fasta (in tophat) was empty.

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

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

Please tell me what I should do.

Thanks.

Answer 1

[Manvendra Singh]

Give multithread options, -p. Maybe your system doesn't have enough memory to run tophat

[cfarmeri]

I gave multithread options -p 3. So the memory may be enough to run tophat.