SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
amplicon sequencing on MiSeq nancysch Illumina/Solexa 20 03-11-2015 11:29 AM
Amplicon sequencing henry.wood 454 Pyrosequencing 20 09-04-2012 07:37 AM
Amplicon sequencing epistatic Ion Torrent 6 07-22-2011 07:43 AM
PubMed: Haplotype-resolved genome sequencing of a Gujarati Indian individual. Newsbot! Literature Watch 1 01-06-2011 12:08 PM
PubMed: Designing deep sequencing experiments: structural variation, haplotype assemb Newsbot! Literature Watch 0 06-23-2010 03:00 AM

Reply
 
Thread Tools
Old 06-25-2012, 01:34 PM   #1
empyrean
Member
 
Location: EU

Join Date: Sep 2010
Posts: 52
Default Haplotype calls from Amplicon Sequencing

Hi.. i have data for two groups.. one group has 10 diffent strains and other group has 5 different strains. 40 genes are selected and primers are designed for these genes. Sequencing is performed on these amplicons which has length of around 300bp. Now i need to identify haplotypes by mapping them to the reference genes. I have to identify haplotypes for each strain as well across the strains. The data i have is reference genes and 454 reads. How to proceed please suggest me.

I mapped the reads using bwa-sw and called the SNPS. This is not working. Tried to use Haploview, hapcut, etc.. but they have their own diff way of input needed like haploview takes input from hapmap project like that.. is there any tool which maps these reads and give haplotypes as output?
empyrean is offline   Reply With Quote
Old 06-25-2012, 01:46 PM   #2
JackieBadger
Senior Member
 
Location: Halifax, Nova Scotia

Join Date: Mar 2009
Posts: 381
Default

http://seqanswers.com/forums/showthread.php?t=18055
JackieBadger is offline   Reply With Quote
Old 06-25-2012, 02:00 PM   #3
empyrean
Member
 
Location: EU

Join Date: Sep 2010
Posts: 52
Default

thankyou for the reply.
jhmc is asking for pcr primers as tags. but i dont know the pcr primers. Also i dont see it constructing a haplotype map. all i have is sequencing reads and reference genes file.
empyrean is offline   Reply With Quote
Old 06-25-2012, 03:27 PM   #4
JackieBadger
Senior Member
 
Location: Halifax, Nova Scotia

Join Date: Mar 2009
Posts: 381
Default

you want to create a haplotype map? Do you mean a minimum spanning or median-joining network network?
As i mentioned before, there is much more to take into consideration. You can not accept sequences as true variants from a reference on the merit of their existence. You need to take into consideration replication, bp mismatch errors, and possibly chimeric sequences.

If I understand what you want to do, SESAME can do this
JackieBadger 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 03:31 AM.


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