Ligating barcodes to amplicons

[lee27]

Hi all,
I am new to the forum and to next-gen in general. I am working on preparing a library of amplicons (20 different amplicons per individual sample - 96 to 180 samples) and I want to barcode the amplicons so that I can identify which individual they are from. Can barcodes/indices be directly ligated to the poly-A tail resulting from PCR or do I first need to blunt the end, apply a poly-A tail and then ligate? Thanks for your thoughts and patience!

[Zaag]

Yes I would alwasy make it blunt end and perform the A-tailing. You could also design fusion primers with the adapter and MID so after PCR you can start emPCR without ligating.