Hello
I have a ShortReadQ object: 
> rfq
class: ShortReadQ
length: 16115723 reads; width: 34 cycles

I used the negation of the result from srduplicated to count the unique reads:
> sum(!srduplicated(sread(rfq)))
[1] 4545719

But also I looked at the frequency with which each read occurs using the tables function:
> head(tables(rfq_s_3_mel)$distribution)
  nOccurrences  nReads
1            1 4022038
2            2  255649

I expected that for nOccurrences=1, the nReads should be the same as what I got with !srduplicated.

Can anybody explain why I got different counts?
Thank you
Joseph Dhahbi


      
	[[alternative HTML version deleted]]

