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: 126.96.36.199 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.