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