Question: Tophat Error: Gtf To Fasta Returned An Error
gravatar for Noel
6.6 years ago by
Noel80 wrote:

Dear all,

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

From running the following command: tophat -p 8 -G genes.gtf -o DIR genome lane1.fastq,lane2.fastq

I get the following:

Beginning TopHat run (v2.0.6)

Checking for Bowtie Bowtie version: Checking for Samtools Samtools version: Checking for Bowtie index files Checking for reference FASTA file Generating SAM header for genome format: fastq quality scale: phred33 (default) Reading known junctions from GTF file Preparing reads left reads: min. length=51, max. length=51, 15308629 kept reads (1316 discarded) Creating transcriptome data files.. [FAILED] Error: gtf_to_fasta returned an error.

I thank you in advance for any help you might provide.


gtf fasta tophat error • 12k views
ADD COMMENTlink modified 4.2 years ago by rodd50 • written 6.6 years ago by Noel80
gravatar for JC
6.6 years ago by
JC8.0k wrote:

A common error in that step is the sequence names in the index and the GTF file don't match.

ADD COMMENTlink written 6.6 years ago by JC8.0k

Even if they were downloaded from Illumina's Igenomes? I will check that nevertheless! Thanks!

ADD REPLYlink modified 6.6 years ago • written 6.6 years ago by Noel80

Never trust downloaded data, first verify it it's the right data and it's complete, large files are likely to be truncated or corrupted when you download them.

ADD REPLYlink written 6.6 years ago by JC8.0k

Hi, I am getting the same error. I have checked the names are same. Also I am using both gtf file and fasta file from ensemble (meaning I don't have different format of chromosomes name). When I am using UCSC index and gtf file everything works well. But UCSC doesn't provide genes name only genes ids. That's why I want to switch to ensembl. I was wondering if you have any idea about this! Or any new progress in the current issue!

ADD REPLYlink written 5.8 years ago by rozita.akramy0
gravatar for hathi
5.9 years ago by
hathi0 wrote:

Hi Noel,

Did you find the answer of your problem, as I am facing the same problem. I checked names of the index and gtf files is same in my case then also i get same error message.

Please share your thought.


ADD COMMENTlink written 5.9 years ago by hathi0

Hi Hathi,

Sorry for my very late reply. I ended up by downloading another reference genome (NCBI instead of UCSC) and then it worked out for me.


ADD REPLYlink written 5.7 years ago by Noel80

hey... i am getting the same error.... from NCBI which referecne geneome did u download ??? please reply

ADD REPLYlink written 4.5 years ago by nikhilvgbt0
gravatar for rodd
4.2 years ago by
London, United Kingdom
rodd50 wrote:

Are there examples of bowtie ref file and the gtf file that match, so I can use them as a reference?

I am having trouble in creating the bowtie index file that matches the GTF file for a specific cytoband of the human genome..

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by rodd50
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