SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Cancer Genomics Advice Raquelle General 9 11-22-2014 03:09 AM
Any advice on RNA bisulfite sequencing? mboth Sample Prep / Library Generation 1 10-06-2011 07:49 AM
advice on methods for comparison Kotoro Bioinformatics 1 07-05-2011 07:35 AM
Advice for beginner govanjarz Bioinformatics 0 06-27-2011 03:53 PM
Requesting advice regarding CAP3 Bharat Bioinformatics 22 06-01-2011 04:09 PM

Reply
 
Thread Tools
Old 05-31-2012, 03:35 AM   #1
nkaushik
Junior Member
 
Location: UK

Join Date: Mar 2012
Posts: 3
Default Sequencing advice

I am planning to sequence 60kb gene using ovelapping long range PCR, I have designed primers and amplified whole gene. I am running into problem now because I am amplifying mixtures of sequences of another gene that is highly homologous (93%) to my gene.

When I sequence mixture of amplified population, will I will be able to characetrize SNPs specific to my gene by aligning to reference genome?
nkaushik is offline   Reply With Quote
Old 05-31-2012, 11:33 AM   #2
bioinfosm
Senior Member
 
Location: USA

Join Date: Jan 2008
Posts: 482
Default

If it is so homologus, you are bound to see mis-alignment. It might be a good idea to check out mappability features for your genes of interest. Perhaps a longer read application would be more suited for you..
__________________
--
bioinfosm
bioinfosm is offline   Reply With Quote
Old 05-31-2012, 01:23 PM   #3
NextGenSeq
Senior Member
 
Location: USA

Join Date: Apr 2009
Posts: 482
Default

Always BLAT your primer sequences prior to having them synthesized. If they map to more than a single region in the genome redesign them.
NextGenSeq is offline   Reply With Quote
Reply

Tags
alignment, pcr sequencing

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 12:58 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO