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Old 01-10-2011, 04:09 PM   #1
nashp
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Location: Calif, US

Join Date: Jan 2011
Posts: 4
Default how does bowtie handle n's in reads? ref sequence?

Hi,
I have reads which have n's and have the hg18 genome sequence which also has a couple of n's. I want to align these reads with the given sequence.

what does 'n' mean and how does bowtie handle this? To be specific, I have a set of reads of which 3/4th contain n's along with agtc. my point is if this is the case, doesn't it affect the alignment time taken since most of the reads turn out as mismatches? I am new to this domain. Could anyone throw some light on this?

Thanks
Nash
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