Tophat Error: Gtf To Fasta Returned An Error

Question

[Noel]

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: 2.0.2.0 Checking for Samtools Samtools version: 0.1.18.0 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.

Noel

Answer 1

[JC]

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

[Noel]

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

[JC]

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.

[rozita.akramy]

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!

Answer 2

[hathi]

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.

thanks

[Noel]

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.

Noel

[nikhilvgbt]

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

Answer 3

[rodd]

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..