Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Reference guided assembly StopCodon De novo discovery 5 06-25-2013 09:49 AM
Assisted de novo genome assembly? Create new consensus mapping reads to reference? zmartine Bioinformatics 8 02-10-2012 12:31 AM
Reference-guided cDNA assembly using related genomes ohofmann Bioinformatics 0 02-08-2011 09:20 AM
Reference-guided alignment crisant Bioinformatics 0 11-27-2010 01:55 PM
MOSAIK - parallel protein sequence guided assembly? liborm Bioinformatics 0 02-08-2010 12:17 PM

Thread Tools
Old 01-10-2011, 08:38 PM   #1
Junior Member
Location: Sydney

Join Date: Aug 2010
Posts: 4
Default bacterial consensus sequence reference guided assembly


I'm trying to generate a consensus sequence, for a bacterial genome, for a reference guided assembly. I've aligned the reads against the reference using Novoalign with SAM output.

I've been playing around with trying to get SAMTOOLS to generate the consensus for me. I'm aware of the pileup2fq option, however, I'm not sure if I can make a pileup file for a single chromosome. Pileup with the -c option automatically assumes you have a diploid organism.

Does anyone know if you can force SAMTOOLS to do what I want to do? For instance, what would you do if you wanted to generate the consensus sequence for a resequencing project for the human Y chromosome?

Any suggestions greatly appreciated...

Many thanks,

Kerensa is offline   Reply With Quote

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 09:50 AM.

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