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Old 09-21-2011, 04:39 PM   #1
cascoamarillo
Senior Member
 
Location: MA

Join Date: Oct 2010
Posts: 160
Default bowtie mapping report

Hi,

Maybe I'm missing some of the bowtie options, but when I map my reads against a pile of contigs (together in a reference file) and when I make the same mapping but only with one contig alone, I do obtain a different number of mapped reads ("reads with at least one reported alignment") for that contig. These are the options I normally use:

bowtie -f --sam --best

Any idea?

Thanks
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