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Old 11-23-2011, 10:06 AM   #1
rcorbett
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Location: canada

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Default tophat max number of junctions per read?

Hi,
I can't seem to find any info that will inform me if there is a maximum number of junctions alignable by a read in tophat. Does anyone know if a single read can span 2 junctions when aligned by tophat? For example, if an exon is 50 bp and a 100 bp read was aligned to it, the read might span the junctions on both sides of the exon. What would tophat do here?

thanks!
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