SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Referance Genome - Noob Question rainmaker Bioinformatics 1 07-06-2013 07:21 AM
Hello from a noob! TabeaK Introductions 0 11-06-2012 12:54 AM
Noob from the land of tartan and tablet pinin4fjords Introductions 0 09-21-2011 06:47 AM
Noob materials geek BBoy Introductions 0 10-18-2010 06:47 PM
Best tool for the job (noob question) bre Bioinformatics 4 01-05-2010 10:56 AM

Reply
 
Thread Tools
Old 02-18-2020, 12:50 PM   #1
dent
Junior Member
 
Location: UK

Join Date: Feb 2020
Posts: 2
Default Noob question: semantics between terms

I'm unsure of the difference between read mapping and contig realignment.

I've seen read mapping being described as putting reads together to form contigs, but have also seen it being described as putting reads together against a reference genome to form a draft genome. This second description is what I think contig (re)alignment describes.

Are they interchangeable?

Thank you!
dent is offline   Reply With Quote
Old 02-19-2020, 03:31 AM   #2
GSviral
Member
 
Location: UK

Join Date: Dec 2014
Posts: 37
Default

For me, I would interpret read mapping as aligning (or mapping) the reads against a reference genome. Putting the reads together to form contigs would be an assembly.

Contig alignment, to me, would be the same idea. Just mapping the contigs to a reference instead of the raw reads.
GSviral is offline   Reply With Quote
Old 02-19-2020, 09:15 AM   #3
dent
Junior Member
 
Location: UK

Join Date: Feb 2020
Posts: 2
Default

Quote:
Originally Posted by GSviral View Post
For me, I would interpret read mapping as aligning (or mapping) the reads against a reference genome. Putting the reads together to form contigs would be an assembly.

Contig alignment, to me, would be the same idea. Just mapping the contigs to a reference instead of the raw reads.
so they're interchangeable to you? is it generally used interchangeably in the field?
dent is offline   Reply With Quote
Old 02-19-2020, 10:51 PM   #4
GSviral
Member
 
Location: UK

Join Date: Dec 2014
Posts: 37
Default

For mapping and alignment I would consider them interchangeable with regards to a reference genome, yeah. If I mentioned either to my colleagues they would understand both just the same. Just the input in your scenario is different - raw reads vs. assembled contigs. Hope this helps!
GSviral is offline   Reply With Quote
Reply

Tags
contig realignment, read mapping

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 04:33 AM.


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