SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
BBDUK and BBMERGE, which goes first chloe1005 Bioinformatics 1 04-12-2018 04:43 AM
Questions concerning bbmerge finswimmer Bioinformatics 1 07-07-2017 04:42 AM
Ligation of Illumina adapters to custom adapters ale Sample Prep / Library Generation 2 02-29-2016 01:42 AM
bbmerge mismatched danova Bioinformatics 3 02-24-2016 12:27 AM
bbmerge ratiomode ? danova Bioinformatics 2 02-16-2016 11:58 AM

Reply
 
Thread Tools
Old 09-08-2018, 09:46 AM   #1
Chief_Lazy_Bison
Junior Member
 
Location: Ames, IA

Join Date: Dec 2014
Posts: 4
Default bbmerge detects different adapters

Hello,

I have some bacterial genomes which were sequenced using the Nextera Flex library prep kit ( insert size ~350 bp) and MiSeq paired end reads (2x300). I want to merge these reads with bbmerge prior to adapter trimming and assembly.

I have used bbmerge's adapter detection feature but have gotten some strange results.
bbmerge seems to detect different adapters on each sample, and many have multiple N's.

The first part of the detected adapter sequence is what Illumina provides as the Nextera Flex adapter sequence, but I'm not sure what the other stuff is.

Here are some of the adapters that were detected:

>Read1_adapter
CTGTCNCTTATACACATCTCCGAGCCCACGAGACGGACTCCTANCTCGTATGCCGTCTTCTGCTTG

>Read2_adapter
CTGTCNCTTATACNCATCTGACGCTGCCGACGAAGAGGANAGNGNNNNNNNNGNNNGNNNC

This is the Nextera Flex adapter sequence given by Illumina CTGTCTCTTATACACATCT

as you can see the first part matches this except for an N stuck in.

Across my 20 samples 16 unique Read1 adapters were detected and
18 unique Read2 adapters were detected.

Should I worry about this? should I feed the detected adapter sequences into bbmerge? should I just give bbmerge the Illumina provided sequence?

Thanks!
Chief_Lazy_Bison is offline   Reply With Quote
Old 09-09-2018, 08:30 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,800
Default

I would suggest that you use the Illumina provided adapter sequence. BBMerge detection feature is good when you don't have that information a priori. There may be some sequencing errors in your reads which is leading to that N insertion.
GenoMax is offline   Reply With Quote
Reply

Tags
bbmerge, bbtools, miseq, nextera flex

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 01:29 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO