how to get rid of singletones

nicedad · 08-19-2011, 01:41 AM

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,

westerman · 08-19-2011, 12:39 PM

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.

nicedad · 08-20-2011, 03:00 AM

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!!

flxlex · 08-22-2011, 01:49 AM

You are in luck: singletons (sequences, that is) are not included in any if the output files, so no need to remove them...

nicedad · 08-23-2011, 05:49 AM

really? this are good news. thanks flxlex.

westerman · 08-23-2011, 05:58 AM

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.

samanta · 08-24-2011, 12:42 PM

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?

nicedad · 08-28-2011, 02:00 AM

Quote:

Originally Posted by samanta

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)?

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08-19-2011, 01:41 AM	#1
nicedad Member Location: Switzerland Join Date: May 2011 Posts: 49	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.

08-24-2011, 12:42 PM	#7
samanta Senior Member Location: Seattle Join Date: Feb 2010 Posts: 109	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

08-19-2011, 12:39 PM	#2
westerman Rick Westerman Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104	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.

08-20-2011, 03:00 AM	#3
nicedad Member Location: Switzerland Join Date: May 2011 Posts: 49	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!!

08-22-2011, 01:49 AM	#4
flxlex Moderator Location: Oslo, Norway Join Date: Nov 2008 Posts: 415	You are in luck: singletons (sequences, that is) are not included in any if the output files, so no need to remove them...

08-23-2011, 05:49 AM	#5
nicedad Member Location: Switzerland Join Date: May 2011 Posts: 49	really? this are good news. thanks flxlex.

08-23-2011, 05:58 AM	#6
westerman Rick Westerman Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104	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.