PCR product quantification

[vl80]

We plan to use uniq adaptor tagged primers for a PCR and then pool PCR products of about 5 samples together for one TruSeq index and follow the TruSeq protocol skipping fragmentation.
Pooling similar or near equal amounts of PCR products (purified) would be a key issue. I would be grateful for reccomendations on quantification methods. And the actual risk of using nano drop for quantitication. Would I be digging my own grave if I use nano drop ? Using any other method would be an additional expense associated

[kwaraska]

Whether or not nanodrop is sufficient will depend on how perfect you need the pooling. If 20% varaince is fine, then nanodrop should be okay.

If you need perfectly equal pooling, I would suggest at least Bioanalyzer/Tape Station and preferrably qPCR.

The extra cost of those should outweigh the need to run the sample again to get sufficient reads.