I was wondering if anyone has run the BowTie2 for the whole genome sequencing data.
My data is paired-end (100-100 bp) and comes from whole genome sequencing. I am not sure at this stage if I should do end-to-end or local-alignment. Any idea anyone? Also, what should be the appropriate value if -M (maximum alignments that bowtie will look for) in order to get the best possible alignment for each read? The default is 3 which seems pretty low to me.