I have a question about tophat2 and bowtie2. I want to align RNA-seq sequencing reads to reference sequences.
My command is like this:
bowtie2 -x genome Brm5.fastq -S Brm5.sam
tophat2 -G genes.gtf -o Brm5_thout genome Brm5.fastq
The read alignment rate of bowtie2 is 45.51%,while tophat2 is only 29.7%. So I am confused. All the data are the same,the tophat2 's result shoud be better than bowtie2 in the theory. Why is this happened, did I set wrong parameters in tophat2?Have anyone meet this kind question.
Any reply will be thankful.