SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
MiSeq Amplified Amplicons sequencing: good Qscore, bad error rate SunPenguin Illumina/Solexa 8 08-08-2016 10:30 PM
PubMed: Error correction of next-generation sequencing data and reliable estimation o Newsbot! Literature Watch 0 07-31-2010 08:56 AM
Per Base Error Rate for Next-Gen Sequencing BertieWooster Bioinformatics 2 12-13-2009 10:03 PM

Reply
 
Thread Tools
Old 01-29-2017, 11:16 AM   #1
JanosMucsi
Junior Member
 
Location: San Francisco

Join Date: Jan 2017
Posts: 1
Default Overall sequencing error rate estimation

Hi,

Given a Jellyfish output, I would like to estimate the overall sequencing error rate. We assume that the unique k-mers in this data set result from a single single-base error, and those are the only sequencing errors in the data set.
Any pointers? Thanks!
JanosMucsi is offline   Reply With Quote
Old 01-29-2017, 09:33 PM   #2
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
Default

You'll get the most accurate results by assembling and mapping to the assembly. But if you want to assume that an error spawns 31 error kmers, then count the total number of kmers with depth less than the bottom of the first trough, and divide by 31, and you'll get a rough approximation of the number of errors. To be more accurate, I would do this (using the BBMap package):

Code:
tadpole.sh in=reads.fq out=contigs.fa
bbmap.sh in=reads.fq mhist=mhist.txt ehist=ehist.txt

Last edited by Brian Bushnell; 01-29-2017 at 09:36 PM.
Brian Bushnell is offline   Reply With Quote
Reply

Tags
error, jellyfish, rate

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 11:39 AM.


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