Can I asked again about paired end reads. I have followed the advice to use only one mate pair. However, it leaves me with a challenge of interpretation. Say I determine that 1e10 bases gives 95% coverage, and this is what I wish to achieve, do I decide:
I need 2e10 bases to achieve this coverage (seems unlikely, since the second mate pair not analysed by nonpareil will contribute more coverage)
I need 1e10 bases (but second mate pair perhaps won't double coverage?)
Something in between
You warned in #8 that if paired end reads are analysed together, the coverage may be underestimated. Having tested this (with the kmer approach), this does not seem to be the case. Perhaps it's because of the kmer approach:
Is there a way to consider even non-overlapping paired reads as a single unit (e.g. concatenate with NNNN between), and would this be desirable?
Can I asked again about paired end reads. I have followed the advice to use only one mate pair. However, it leaves me with a challenge of interpretation. Say I determine that 1e10 bases gives 95% coverage, and this is what I wish to achieve, do I decide:
You warned in #8 that if paired end reads are analysed together, the coverage may be underestimated. Having tested this (with the kmer approach), this does not seem to be the case. Perhaps it's because of the kmer approach:
Is there a way to consider even non-overlapping paired reads as a single unit (e.g. concatenate with NNNN between), and would this be desirable?
Thanks for your help,
Andrew