I actually have three minor questions about bowtie. I wrote a run.sh file as follows:
bowtie2-build rrna.fa rRNA bowtie2 --very-sensitive -x rRNA -f reads.fa --un a.fa bowtie2-build genome.fa GENO bowtie2 --very-sensitive -x GENO -f a.fa --un b.fa
However, when running bash run.sh, I was encountered a problem as follows. This is my first question.
Could not locate a Bowtie index corresponding to basename "GENO"
Error: Encountered internal Bowtie 2 exception (#1)
My second question is related to bowtie --very-sensitive option. Does this option map more reads on the genome?
My third question is about bowtie vs tophat. My understanding is: bowtie can not detect exon splicing, so abandoned some mapping reads; in contrast, Tophat overcomes this problem and enables more reads mapping on genome. Is my understanding right?
THANK YOU very much!