SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
PolyA removal from RNA seq Illumina reads figo1019 Illumina/Solexa 2 11-18-2012 06:06 PM
Sigma Genomeplex Whole genome amplification primer removal JueFish Bioinformatics 3 09-20-2012 03:06 PM
removal of primer dimers. shurjo Sample Prep / Library Generation 2 07-08-2011 02:12 PM
Illumina primer immobilization howiewang Illumina/Solexa 1 06-02-2011 04:54 AM
Primer removal tool for next gen? Shruti Madhiwalla Bioinformatics 3 03-24-2011 02:37 AM

Reply
 
Thread Tools
Old 09-01-2017, 10:46 AM   #1
bio_informatics
Senior Member
 
Location: USA

Join Date: Nov 2013
Posts: 181
Default Doubt for primer removal: illumina

Hi All,

I was browsing online bioinformatics forum and stumbled onto query about primer, adapters that put me in thought about the process/pipeline I'm performing. I've Illumina paired-end 100bp, whole-genome bacterial data.

I assemble these reads using denovo assembler, things look good. But in an earlier step I trim these using trimmomatic tool, using an adapter file provided by sequencing center.

However, I never remove primers.
I'm wondering why I didn't remove primers, nor did I see any issue in my downstream analysis of ST identification, phylogenetic trees.

Should I not remove primers? Why?
__________________
Bioinformaticscally calm
bio_informatics is offline   Reply With Quote
Old 09-01-2017, 12:47 PM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,548
Default

See if this primer helps.
GenoMax is offline   Reply With Quote
Old 09-01-2017, 03:44 PM   #3
luc
Senior Member
 
Location: US

Join Date: Dec 2010
Posts: 305
Default

The primer sequences will match part of the full adapter sequences (or their reverse complement). Thus adapter trimming will usually be just fine. "Free" primers should not show up in your sequence data.
luc is offline   Reply With Quote
Reply

Tags
adapter, illumina, primer

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 01:41 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO