I am trying to use tophat to align my fastq reads to the reference genome.
I first used bowtie to create index files. I have trimmed my read1 and read2 fastq files. All output files of bowtie index and read files are in the same directory. Here you can see the screen shot of my directory.
Then I am running the following command to run tophat.
tophat -p 8 -G genome.gtf -o sample_thout genome SAMPLE_R1.fq SAMPLE_R2.fq
I do not know what I am doing wrong since my command runs but after almost 45 minutes it stops.
The sample_thout directory only contains the following files.
Inside the tmp folder I can see the following:
inside the logs folder I can see the following files:
So I can not run tophat properly to get the desired output. I am pretty new to RNA seq and using tophat. Does anybody have any idea what is my mistake?