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 commad is following:
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 proble.