SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
how to get rid of adapter sequences asheenlevrai General 4 01-03-2012 06:46 AM
getting rid of 0 entries in bedTools genomeCoverageBed tool efoss Bioinformatics 4 07-18-2011 07:17 PM

Reply
 
Thread Tools
Old 08-19-2011, 01:41 AM   #1
nicedad
Member
 
Location: Switzerland

Join Date: May 2011
Posts: 49
Default how to get rid of singletones

Hi everyone,
After mining the file 454NewblerMetrics.txt I found 134002 singletones my question is whether this number sounds normal?? and how to get rid of these? with which tool?

thanks in advance,

Last edited by nicedad; 08-19-2011 at 01:47 AM.
nicedad is offline   Reply With Quote
Old 08-19-2011, 12:39 PM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

That number doesn't sound too bad. Looking at a recent run we had 720K reads of which 240K were singletons and the most of the rest collapsed into assemblies.

As for how to get rid of them, look at the 454ReadStatus.txt file. From that you can separate the reads into Assembled, Partially Assembled, Singletons, etc.
westerman is offline   Reply With Quote
Old 08-20-2011, 03:00 AM   #3
nicedad
Member
 
Location: Switzerland

Join Date: May 2011
Posts: 49
Default

Thanks westerman. my problem is I could not figure out the principle of how to get rid of these from the 454Allcontigs file? I mean, what is the correlation between singletons in 454ReadStatus and 454Allcontigs since the later one will be used for further analysis.
Ok, I separated them (with grap) but what I got are only the name of all singletons and not sequences!!
sorry unconveniece as am getting my feet wet in this domain.

However, how is the wether in Indiana right now, I was a grad student in Indy!!
nicedad is offline   Reply With Quote
Old 08-22-2011, 01:49 AM   #4
flxlex
Moderator
 
Location: Oslo, Norway

Join Date: Nov 2008
Posts: 415
Default

You are in luck: singletons (sequences, that is) are not included in any if the output files, so no need to remove them...
flxlex is offline   Reply With Quote
Old 08-23-2011, 05:49 AM   #5
nicedad
Member
 
Location: Switzerland

Join Date: May 2011
Posts: 49
Default

really? this are good news. thanks flxlex.
nicedad is offline   Reply With Quote
Old 08-23-2011, 05:58 AM   #6
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

I meant to reply but the weekend got in the way. flxlex is correct in that the Singletons are not included in the 454AllContigs file. In fact for our customers we make up a new file that includes both the contigs and the singletons so that they have a "one stop" method of seeing all of their relevant data. After all just because a read is classified as a Singleton because it can not align with any other read does not make the Singleton read irrelevant.
westerman is offline   Reply With Quote
Old 08-24-2011, 12:42 PM   #7
samanta
Senior Member
 
Location: Seattle

Join Date: Feb 2010
Posts: 109
Default

Agree with other experts. Singletons are single people (reads), who did not find some other read to marry. That does not make them bad people (reads) by any measure.

Do you want to eliminate them all? What kind of world will that be like?
__________________
http://homolog.us
samanta is offline   Reply With Quote
Old 08-28-2011, 02:00 AM   #8
nicedad
Member
 
Location: Switzerland

Join Date: May 2011
Posts: 49
Default

Quote:
Originally Posted by samanta View Post
Agree with other experts. Singletons are single people (reads), who did not find some other read to marry. That does not make them bad people (reads) by any measure.

Do you want to eliminate them all? What kind of world will that be like?
If singletones are useful, they would not be removed from 454Allcontigs file!
Furthermore, I wana remove them because this is done in the almost manuscrits of this area of research, if you want I can post some.

However, does anyone know how to get their weight (Mb)?
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 03:58 PM.


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