SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
forward and backward neighbors !!!! arun raj General 0 01-17-2012 12:12 AM
Separate forward and reverse coverage in Artemis nivea Bioinformatics 4 12-12-2011 03:20 AM
how to define a forward or reverse read file poorphd Illumina/Solexa 3 11-22-2011 12:34 PM
How to separate coverage of forward and reverse reads on same axis? Kennels Bioinformatics 6 05-04-2011 12:12 AM
bias in mapped forward/reverse read ratios dvh Illumina/Solexa 8 10-02-2008 07:32 AM

Reply
 
Thread Tools
Old 02-04-2009, 09:29 PM   #1
asankaf
Member
 
Location: clayton

Join Date: Jan 2009
Posts: 10
Default forward and reverse sequance

in most of the mutation detection software tools we need to provide forward and reversce trace files along with the reference sequence files.
What is this forward/reverse trace files and why we use this kind of aproach?
asankaf is offline   Reply With Quote
Old 05-26-2009, 06:36 AM   #2
Melissa
Senior Member
 
Location: Switzerland

Join Date: Aug 2008
Posts: 124
Default

That's the Sanger's way to detect SNPs. All Sanger sequencing requires the forward and reverse primer of the amplicon. The forward sequences are sequenced from the forward primer and vice versa. Therefore, both forward and reverse sequences should reverse complement each other.

Say, you want to detect SNPs in individual 1 & 2. You have forward and reverse sequences from both individuals (shown below). At first look, it seems like there's a T/C SNPs. But, there's a high probability that base C in sequence 2F is a sequencing error because it's not present in the reverse strand.

1F - AATAA
2R - AATAA
2F - AACAA
2R - AATAA

SOLiD can detect the orientation of the reads. I was told that this is one of the advantage of SOLiD over other platforms. I really don't see the importance. Any thoughts?
Melissa is offline   Reply With Quote
Old 05-26-2009, 09:29 AM   #3
swbarnes2
Senior Member
 
Location: San Diego

Join Date: May 2008
Posts: 912
Default

Quote:
Originally Posted by Melissa View Post
SOLiD can detect the orientation of the reads. I was told that this is one of the advantage of SOLiD over other platforms. I really don't see the importance. Any thoughts?
I think it's helpful in RNA-seq, or maybe small RNAs?

It doesn't matter much for DNA sequencing.
swbarnes2 is offline   Reply With Quote
Old 05-26-2009, 11:18 AM   #4
sklages
Senior Member
 
Location: Berlin, DE

Join Date: May 2008
Posts: 628
Default

SOLiD can distinguish between a simple sequencing error and a SNP, as there must be at least two changes in colorspace to change one base in basespace. That's the advantage of SOLiD.

cheers,
Sven
sklages is offline   Reply With Quote
Old 05-26-2009, 07:41 PM   #5
Melissa
Senior Member
 
Location: Switzerland

Join Date: Aug 2008
Posts: 124
Default

Quote:
Originally Posted by swbarnes2 View Post
I think it's helpful in RNA-seq, or maybe small RNAs?

It doesn't matter much for DNA sequencing.
I was informed that it'll be helpful in RNA-seq too. Two genes that are located next to each other can be distinguished if they are transcribed in different direction. Quite an unique situation. Don't think it will be useful for most people.
Melissa is offline   Reply With Quote
Old 05-27-2009, 07:48 AM   #6
Pepe
Member
 
Location: Germany

Join Date: Mar 2009
Posts: 28
Default

Having orientation does not seem very important because most experiments don't have the ability to see it. I bet there are many interesting surprises once it becomes a standard.
For example, I've heard people doing RNA-seq experiments and finding reads in reverse orientation that align to introns from some genes. No clue what they are there for...
Pepe 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 11:28 AM.


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