SEQanswers

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



Similar Threads
Thread Thread Starter Forum Replies Last Post
Illumina adapter trimming figo1019 Illumina/Solexa 12 06-03-2014 11:32 AM
Do not use "adapter trimming" in MiSeq Reporter 2.0.25 ECO Illumina/Solexa 9 12-10-2013 04:38 AM
FASTXtoolkit adapter trimming Mark Bioinformatics 36 10-24-2013 10:28 AM
Adapter Trimming Nextera mm.perrineau Illumina/Solexa 1 09-12-2012 10:56 AM
3' Adapter Trimming caddymob Bioinformatics 0 05-27-2009 12:53 PM

Reply
 
Thread Tools
Old 09-18-2012, 06:23 AM   #1
microgirl123
Senior Member
 
Location: New England

Join Date: Jun 2012
Posts: 197
Default Basic adapter trimming question - MiSeq

Hi, I'm new to next-gen sequencing and we have a nice, new MiSeq. Although, I've seen the post about not using adapter trimming on the MiSeq I think our customers might want to. We're mostly just doing PCR amplicons (not human) and bacterial resequencing and assembly. How do I know if adapter trimming needs to be done? Any information about adapter trimming would be great! I'm pretty good with the basics of how to run the MiSeq but hazy on the software/bioinformatics ends of things!
microgirl123 is offline   Reply With Quote
Old 09-18-2012, 08:34 AM   #2
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,358
Default

Search and read some more. Assuming you're using "standard" adapters and library prep, you should trim adapters if a significant portion of your inserts are shorter than your read lengths (thus reading into the distal adapter).

Also, if you're sequencing amplicons, you should certainly trim out (or at least be aware of), the primer sequences as they are entirely sequence of synthetic DNA.
ECO is offline   Reply With Quote
Old 09-18-2012, 09:15 AM   #3
microgirl123
Senior Member
 
Location: New England

Join Date: Jun 2012
Posts: 197
Default

Thanks ECO! This whole first run has been a learning experience/problem. When the MiSeq was installed and I was trained we only had the v1 chemistry. Now that we have the v2 chemistry (but not the hardware update), my inserts are too small. So I had only ~200-300 bp inserts but did 2x250 reads. I think this probably led to me reading into my adapter in some cases. I also had a huge hangup with the Velvet assembler because of the massive overlap in reads!
microgirl123 is offline   Reply With Quote
Reply

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 10:19 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO