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Tophat error on using NONCODE database gtf file.

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

rna-seq
• 3,150 views • link
updated by Ram Ram • written by cfarmeri 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.

• 0 views • link
updated by Ram Ram • written by cfarmeri cfarmeri

1 answer

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

• 0 views • link
updated by Ram Ram • written by Manvendra Singh Manvendra Singh

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

• 0 views • link
updated by Ram Ram • written by cfarmeri cfarmeri

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