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Old 08-13-2011, 10:06 PM   #1
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Location: Canada

Join Date: Aug 2011
Posts: 3
Default target mapped read percentage

I am a newbie to sequencing and apologies in advance if my question is too simple.
We are working on yeast genome (it has only 12M base pairs and low repetition) and sequenced it with very high coverage. We are trying lots of alignment(bowtie, shrimp, etc) + snp finder(varid, gatk, samtools). It seems like we are in a parameter jungle.

As a first step, what is the expected percentage of reads I should get with paired end mapping?
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