Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
DESeq2 - COLUMN and ROWS number don't match KYR RNA Sequencing 1 07-16-2014 02:21 PM
Too little reads mapped back to contigs using Bowtie oliviaxinw Bioinformatics 4 09-28-2012 06:18 AM
Can bowtie align mates individually if they don't match? history_of_robots Bioinformatics 1 02-06-2012 06:01 AM
How to allow mapped contigs to be used in de novo assembly projects edleloth 454 Pyrosequencing 1 03-08-2011 08:13 AM
454IsotigsLayout.txt - contigs don't match to any isotig? dschika Bioinformatics 9 10-11-2010 05:58 AM

Thread Tools
Old 09-24-2015, 02:05 PM   #1
Junior Member
Location: USA

Join Date: Sep 2015
Posts: 1
Default de novo contigs don't match mapped reads

Hi all,

I'm confused about the results I get when I map the reads back to the contigs from Abyss. There are a number of contigs where the majority of reads have a different base than the contig at a given position. I don't understand how the assembler would assign a base to a position if it is not supported by the reads.

Thanks for any explanations.

bdorsey is offline   Reply With Quote
Old 09-25-2015, 12:39 AM   #2
Senior Member
Location: Geneva

Join Date: Feb 2012
Posts: 179


maybe you have more reads supporting the base at this position than reads which don't support it? Different possibilities to check this: the fastest (if you already have a pipeline for) would be to do a fast SNP calling using your contigs as reference...

SylvainL is offline   Reply With Quote

abyss, contigs, mapping reads, mismatches

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 08:18 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO