I got a little confused trying to visualize my bowtie2 mapped reads. I mapped some short (synthetic) RNA reads to a self-made (short) reference sequence with bowtie2, and I have aquired the .bam file.
Now I want to visualize this .bam file. I wanted to do this with IGV, however they want me to also provide a 'genome sequence' (which I understood is the reference sequence). Isn't the reference sequence already provided in the .bam file? Why do I need to provide a reference sequence again? I just want to visualize the mapping bowtie2 did.
I'd have to read more of the manuals of IGV but I can't seem to find an answer to this question. If there is an informaive page that could help me with this specific question I'd also be very happy!
Thanks in advance!