SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Merging paired ends fastq files with BBMerge bi_maniac Illumina/Solexa 19 11-04-2015 02:43 AM
Moderately Low Yield ChIP jazz710 Sample Prep / Library Generation 9 01-22-2015 11:18 AM
Nextera XT low yield nicoT Sample Prep / Library Generation 2 12-09-2014 12:17 PM
Low library yield Seqwork RNA Sequencing 2 03-06-2014 11:57 AM
Low yield with Ampure XP cleanup akbowser Sample Prep / Library Generation 5 08-27-2012 06:08 AM

Reply
 
Thread Tools
Old 11-13-2018, 05:09 AM   #1
omer_a
Junior Member
 
Location: Israel

Join Date: Nov 2017
Posts: 1
Default Very low merging yield with BBMerge vs PEAR

Hey all,
I'm trying to merge my reads (300bp, demultiplexed) using BBMerge and for my samples, sequencing results of the fungal ITS2 region, BBMerge yields much lower merged reads compared to PEAR (~50% vs ~90%, respectively). Most of the unmerged reads by BBMerge are ambiguous. Few questions:
Is there something I can try with BBMerge?
I've read here that PEAR results in a lot of FP, but can it be up to 50% of the sample?
Many of my reads are longer than the actual length of the fragment sequenced (ITS2 region vary in size, 100-500bp), is BBMerge sensitive to post-adapters "garbage" bases?

I'd rather not to trim my reads based on quality \ primers' sequence since it interferes with follow steps of the analysis.

Thanks,
Omer
omer_a is offline   Reply With Quote
Old 11-13-2018, 06:26 AM   #2
Phoenix_ICE
Member
 
Location: UK

Join Date: Jan 2011
Posts: 13
Default

FLASh is a good choice to try.
https://ccb.jhu.edu/software/FLASH/

Last edited by Phoenix_ICE; 11-13-2018 at 06:33 AM. Reason: grammar
Phoenix_ICE 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 07:23 PM.


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