5'adaptor trimming of microRNA sequence data

Question

[evimeng]

I lost about 50% of my reads during 5'adoptor trimming of microRNA-Seq data. I used cutadapt program. I don't understand why. Has anyone noticed a similar trend in the past? What can I do to reverse the situation? Thanks for your comments. Eve

Answer 1

[mark.ziemann]

It could be that the self ligated adapter construct the is most abundant fragment in the library. You can check this by grepping the adapter string and seeing whether the adapter begins at the start of the read or whether mostly there are 20-22 mers (miRs) before the adapter. If most of the reads are self-ligated adapter, then they can't be used downstream. You can reverse the situation by size selecting the library again by PAGE (6% Novex).