why remove adapter just from 3' of the reads

Question

[jonessara770]

Hello,

I wonder why we just remove adapter from 3' end of reads and not both sides? For example when using Illumina TruSeq™ Small RNA, they use RA5 and RA3 adapter, so why we just trim 3'?

For small RNA, do you trim for quality from both sides of a read if both sides does not have good quality?

Thanks Sara

Answer 1

[GenoMax]

Take a look at the figure at the bottom of this page: http://nextgen.mgh.harvard.edu/IlluminaChemistry.html Unless your inserts are shorter then the length of sequencing you should never see adapters except on the 3'end.