Handling of singletons in Cufflinks

jhb1980 · 10-28-2011, 06:36 AM

Hello,

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,

Jan

G0G1r1 · 09-20-2020, 12:51 PM

THX A LOT for this thread

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10-28-2011, 06:36 AM	#1
jhb1980 Junior Member Location: Switzerland Join Date: Dec 2010 Posts: 7	Handling of singletons in Cufflinks Hello, 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, Jan

09-20-2020, 12:51 PM	#2
G0G1r1 Junior Member Location: Spain Join Date: Sep 2020 Posts: 1	THX A LOT for this thread