Truseq 5' adapters

[Vinn]

Hi folks

I am a newbie trying to trim adapters from my fungal genome data. It is generated with TruSeq PCR-free 350 bp insert/Hiseq 2500 (250 PE). I read manuals of some trimmers and it seems they all focus on removal of adapters from 3' end. But what about adapters on 5' end? Shouldn't we concern about them?

Thank you so much in advance for all answers and explanations.

[nucacidhunter]

Reads start from 5' end of DNA strand so adapters will be at the 3' end of read if the library fragment insert was shorter than cycle number. Adapter at 5' end includes the sequencing primer binding site just before insert.

[Brian Bushnell]

BBDuk will happily remove adapters from the 5' end using the flag "ktrim=l". But as nucacidhunter stated, those are atypical and probably not of concern unless you are doing deep multiplexing with inline barcodes or an unusual long-mate pair library.