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Old 09-15-2009, 08:01 AM   #1
warrenemmett
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Location: South Africa

Join Date: Nov 2008
Posts: 23
Default Can paired-end mapping produce more reads than single-end ?

Hi,

I am currently mapping 75bp paired end data to a cDNa library. I have heard that there is a chance there are chimeras in a large portion of the reads and as such have had to change to single end analysis.

My results seem to show that I have less hits (I counted reads mapped in both paired and single end alignment) in single-end alignment (using bowtie).

Does anyone know if this is infact possible or more likely an error in the code?
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