Bowtie2 For Whole Genome Sequence

Question

[vinay kumar]

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.

Thanks

Answer 1

[Lee Katz]

You should trim low quality off the ends of your reads (and filter your reads too), followed by end-to-end alignment. Trimming should obviate any need for local alignment.

M should vary according to how repetitive your genome is. Do you expect the average read to hit against more than 3 places? How often does a 100-mer occur in your genome?

[vinay kumar]

Thanks, Lee. My data is from human genome.... I can calculate the occurrence of 100 bp read in the genome but the problem is the paired-end data. So I am not sure what value to choose for "M"?

[Lee Katz]

Human genome... not my forte. Maybe someone else could explain what to choose for M in this situation.