Question: Bowtie2 For Whole Genome Sequence
0
gravatar for vinay kumar
7.9 years ago by
vinay kumar0 wrote:

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

genome bowtie2 • 2.7k views
ADD COMMENTlink written 7.9 years ago by vinay kumar0
0
gravatar for Lee Katz
7.9 years ago by
Lee Katz3.0k
Atlanta, GA
Lee Katz3.0k wrote:

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?

ADD COMMENTlink written 7.9 years ago by Lee Katz3.0k

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"?

ADD REPLYlink written 7.9 years ago by vinay kumar0

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

ADD REPLYlink written 7.9 years ago by Lee Katz3.0k
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