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Old 10-28-2011, 06:36 AM   #1
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Default Handling of singletons in Cufflinks


Just a quick question that I couldn't seem to find a conclusive answer to:

How (if at all) does Cufflinks treat reads from a paired-end RNA Seq experiment that failed to be 'properly' paired (i.e. singletons)?

I assume by nature and definition of FPKM, these will not be considered for abundance estimation of a given transcript? But do they in any form contribute to any other aspect of Cufflinks, e.g. transcript assembly or confidence estimations?

Thank you,

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Old 09-20-2020, 12:51 PM   #2
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THX A LOT for this thread
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