Doubt for primer removal: illumina

bio_informatics · 09-01-2017, 09:46 AM

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?

GenoMax · 09-01-2017, 11:47 AM

See if this primer helps.

luc · 09-01-2017, 02:44 PM

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.

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09-01-2017, 09:46 AM	#1
bio_informatics Senior Member Location: USA Join Date: Nov 2013 Posts: 182	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

09-01-2017, 11:47 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 6,784	See if this primer helps.

09-01-2017, 02:44 PM	#3
luc Senior Member Location: US Join Date: Dec 2010 Posts: 337	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.