SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
something wrong when using consed dingkai0564 Bioinformatics 0 08-25-2011 12:05 AM
Consed would not run in 10.6 YongLi Bioinformatics 0 02-10-2011 08:21 AM
Errors using consed Mona Bioinformatics 1 09-22-2010 01:43 AM
consed issues with newbler generated hybrid assembly greigite Bioinformatics 8 08-23-2010 11:57 AM
454 assembly using consed mjleaks Bioinformatics 7 08-28-2009 02:52 AM

Reply
 
Thread Tools
Old 06-10-2011, 04:28 AM   #1
nicedad
Member
 
Location: Switzerland

Join Date: May 2011
Posts: 49
Default why consed after Newbler

Hi everyone,
I'm just getting my feed wet with NGS thus my questions usualy appear to be very naive.

My question this time is, why one should use another tool i.e. CONSED to deal with the result of an assembler i.e. Newbler even though the later
does the trimming and removes the primers?

thanx in advance.
nicedad is offline   Reply With Quote
Old 06-10-2011, 05:15 AM   #2
nickloman
Senior Member
 
Location: Birmingham, UK

Join Date: Jul 2009
Posts: 356
Default

For viewing the assembly, designing finishing primers, joining contigs together etc.

It's not a required step if you want to just deal with the draft contigs.

Quite helpful though. You can use other viewers (Tablet, for example) for viewing the assembly if you prefer.
nickloman is offline   Reply With Quote
Old 06-10-2011, 05:26 AM   #3
nicedad
Member
 
Location: Switzerland

Join Date: May 2011
Posts: 49
Default

Quote:
Originally Posted by nickloman View Post
For viewing the assembly, designing finishing primers, joining contigs together etc.
Necloman, thanks a lot for the replay. could you plese advise, why one should
join the contigs to gether since we already get the consensus?

Quote:
Originally Posted by nickloman View Post
You can use other viewers (Tablet, for example) for viewing the assembly if you prefer.
really nice tool will check it
nicedad is offline   Reply With Quote
Old 06-10-2011, 05:40 AM   #4
nickloman
Senior Member
 
Location: Birmingham, UK

Join Date: Jul 2009
Posts: 356
Default

Quote:
Originally Posted by nicedad View Post
Necloman, thanks a lot for the replay. could you plese advise, why one should
join the contigs to gether since we already get the consensus?
Well, presumably your assembly is in fragments.

In some circumstances you may want to join those together through some finishing experiments, perhaps there's a region of particular interest and it is split in two by a repeat.

If you are lucky enough to have the assembly in a single contig then you don't need to do this, but it's pretty unusual!
nickloman is offline   Reply With Quote
Old 06-10-2011, 11:08 AM   #5
nicedad
Member
 
Location: Switzerland

Join Date: May 2011
Posts: 49
Default

Do you mean that contigs must be joined to analyse a cDNA?
if yeah, how to join them if the data are many Mbs?

best,
nicedad is offline   Reply With Quote
Old 06-10-2011, 12:19 PM   #6
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

cDNAs are usually from mRNA (transcripts of protein expression) and thus are short, on the order of 1000 base contigs. A 454 project using Newbler with the '-cDNA' flag is excellent for creating complete contigs that can not and should not be further merged. We use Blast2Go to annotate our 454 runs.

On the other hand, a whole genome shotgun assembly will almost always produce many contigs which can then be merged together into chromosomes (at least in theory) or at the very least into longer contigs. Using Consed or other tools will help scaffold and merge those contigs together or at least tell you what further work to do in order to get good merging.

How to join them together? Usually requires more sequencing. Either directed or random. And much hoping that repeats don't get in the way. "Finishing" is a tough human-labor-requiring problem -- that is why there are so many unfinished genomes out there.
westerman is offline   Reply With Quote
Old 06-11-2011, 03:21 AM   #7
nicedad
Member
 
Location: Switzerland

Join Date: May 2011
Posts: 49
Default

nickloman, westerman, thanks for your patience!
nicedad 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 08:14 PM.


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