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Old 11-01-2012, 08:04 AM   #6
nr23
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Location: Ireland

Join Date: Oct 2012
Posts: 42
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I ran the 65bp trimmed reads through FLASH (http://genomics.jhu.edu/software/FLASH/index.shtml) to confirm that, post trim, there's no overlap.

As I understand it bowtie and tophat map the pairs independently, so I would expect that dispensing of 1/2 of my reads would result in the same % mapped reads, maybe I'm wrong though?

My primary concern is that the % of reads mapped is so low, I'm less concerned about the pairing of the reads (I'm interested in differential expression rather than resolving isoforms etc) but can't help but feel that the two are linked...
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