I'm somewhat new to bioinformatics, so please bear with me.
I'm running tophat2 on some fastq files using the HG38 as reference. This is the command that I ran:
tophat2 --b2-sensitive -G /home/fadhil/hg38_ref/lib/hg38.refGene.gtf -p 16 -o /home/data/mcf10_tophat_output /home/fadhil/Bowtie2Index/genome ./SRR925720_mcf10a.fastq
It takes about 8 hours, but in the end the mapping rate is almost 0%, it maps 3997 out of 31898079 reads. I'm not sure I understand why this is happening, although tophat emitted the following error consecutively as it was running:
Warning: Encountered reference sequence with only gaps
Ignoring any potential errors with the fastq files themselves, what could possibly be the problem here?