Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa

Similar Threads
Thread Thread Starter Forum Replies Last Post
TruSeq methylated adapters? epistatic Illumina/Solexa 5 03-24-2016 09:24 AM
4C-seq with Truseq adapters on Nextseq500 problem Asashoryu Illumina/Solexa 7 06-19-2015 10:57 PM
Remove Illumina TruSeq Index adapters enrico16 Bioinformatics 0 01-14-2015 01:56 AM
Homemade TruSeq adapters sebbaba Illumina/Solexa 2 09-09-2013 09:26 AM
Using TruSeq adapters with older protocols- not working? jlove Illumina/Solexa 2 12-01-2011 01:11 PM

Thread Tools
Old 09-21-2016, 01:22 PM   #1
Location: Sweden

Join Date: Nov 2014
Posts: 18
Default Truseq 5' adapters

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.
Vinn is offline   Reply With Quote
Old 09-21-2016, 02:39 PM   #2
Jafar Jabbari
Location: Melbourne

Join Date: Jan 2013
Posts: 1,238

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.
nucacidhunter is offline   Reply With Quote
Old 09-22-2016, 10:18 AM   #3
Brian Bushnell
Super Moderator
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

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.
Brian Bushnell is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 01:50 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO