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
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