SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
Generate consensus sequence with Samtools mpileup? Heisman Bioinformatics 4 10-28-2013 04:57 PM
Help needed to generate Consensus from alignment sarbashis Illumina/Solexa 0 08-10-2011 09:58 PM
BAM/SAM to a gapped multiple sequence alignment query Bioinformatics 6 04-06-2011 05:07 AM
Generate subset from BAM format ForeignMan Genomic Resequencing 4 02-28-2011 06:20 AM
Consensus part from sequence read(fastq) and align(BAM) files culmen Bioinformatics 5 12-21-2010 03:57 AM

Reply
 
Thread Tools
Old 09-13-2011, 06:06 AM   #1
Adam Witney
Junior Member
 
Location: London

Join Date: Mar 2011
Posts: 8
Default Generate consensus sequence from BAM alignment

Hi,

I have a BAM file and I would like to generate a consensus sequence or a set of contigs (if there are gaps in the alignment). My google search seems to only come up with generating consensus reads... are there any tools that can produce contigs?

Thanks

adam
Adam Witney is offline   Reply With Quote
Old 09-14-2011, 12:46 AM   #2
francois.sabot
Member
 
Location: France

Join Date: Dec 2009
Posts: 41
Default

Hi
One overcome for that is to generate a VCF file from BAM and then extrapolate your sequence based on your ref. We have performed that using a simple home-made script and VCF file with all site expressed (you juste need to extract the 5th column). Gaps will be points, you can cut your contig if more than 20 points appear, eg.

Some tools such as NovelSeq seem to be able to 'fill the gaps', ie to add the extra sequences from the sequenced target vs the ref sequence.

Hoping it will help

F.
__________________
Francois Sabot, PhD

Be realistic. Demand the Impossible.
www.wikiposon.org
francois.sabot is offline   Reply With Quote
Old 09-14-2011, 02:49 AM   #3
Adam Witney
Junior Member
 
Location: London

Join Date: Mar 2011
Posts: 8
Default

thanks for the advice, I'll give it a try

adam
Adam Witney 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 09:21 AM.


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