SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
3' trimming using cutadapt changes property of 5'. Alex Lee RNA Sequencing 0 04-17-2014 10:28 PM
Adapters trimming: Cutadapt vs Trimmomatic MafaldaSF Bioinformatics 8 03-20-2014 06:16 AM
Using CASAVA versus cutadapt for adapter trimming id0 Bioinformatics 0 08-08-2013 09:39 AM
Adapter trimming and trimming by quality question alisrpp Bioinformatics 5 04-08-2013 04:55 PM
What is a good mapping quality cutoff? LP_SEP23 Bioinformatics 1 03-06-2012 06:28 AM

Reply
 
Thread Tools
Old 08-13-2014, 06:24 AM   #1
bongbimit
Member
 
Location: Ha Noi

Join Date: Dec 2013
Posts: 29
Default cutadapt quality trimming cutoff algorithm

Hi all,
I 've use cutadapt to pre-processing my data but i have 2 quenstion about algorithm of quality trimminh in cutadapt:

1)Will Cutadapt scan from 3' end of read?
2)If scan from 3' end, is quality threshold (eg: 20) count by average quality or from which algorithm

Thanks in advance.
bongbimit is offline   Reply With Quote
Old 08-13-2014, 08:36 AM   #2
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
Default

I posted a graph here comparing various quality trimming algorithms. Cutadapt was better than fastx and prinseq but outperformed by sickle, seqtk, and BBTools (the latter two use the Phred algorithm).

I'm not sure exactly what algorithm cutadapt is using, but it appears to perform better than simply stopping at the first base above a threshold.
Brian Bushnell 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 12:57 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO