Confusing about definition of singleton in transcriptome assembly

bongbimit · 09-19-2014, 02:18 AM

Hi all,
I am working about denovo assembly of non-model organism by Trinity assembler but i still confusing of definition's "singleton".

Definition 1: Some papers and journals define singleton: TGICL cluster contig(transcripts) from Trinity's output and we have 2 class is "Cluster" and "Singleton". (http://www.plosone.org/article/info%...l.pone.0014233)

Definition 2: But when i read some website or blog i realize singleton is reads which do not overlap with other reads in assembly process

So which 's definition right? and if "definition 2" 's right, how to extract "non-overlap reads" from Trinity's output (transcripts)

Thanks in advance.

reema · 09-22-2014, 08:04 AM

Hello,

Please see this link :- http://seqanswers.com/forums/showthread.php?t=46711. Well I was also very much confused about singleton. As rick mentioned in this post that align reads without mate(pair) reads are known as singletons. I am agree with him. But 72,424 singletons in this plos one paper, make me curious to known more about singletons.

Thanks,
Reema,

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09-19-2014, 02:18 AM	#1
bongbimit Member Location: Ha Noi Join Date: Dec 2013 Posts: 29	Confusing about definition of singleton in transcriptome assembly Hi all, I am working about denovo assembly of non-model organism by Trinity assembler but i still confusing of definition's "singleton". Definition 1: Some papers and journals define singleton: TGICL cluster contig(transcripts) from Trinity's output and we have 2 class is "Cluster" and "Singleton". (http://www.plosone.org/article/info%...l.pone.0014233) Definition 2: But when i read some website or blog i realize singleton is reads which do not overlap with other reads in assembly process So which 's definition right? and if "definition 2" 's right, how to extract "non-overlap reads" from Trinity's output (transcripts) Thanks in advance.

09-22-2014, 08:04 AM	#2
reema Member Location: Scotland Join Date: Feb 2014 Posts: 27	Hello, Please see this link :- http://seqanswers.com/forums/showthread.php?t=46711. Well I was also very much confused about singleton. As rick mentioned in this post that align reads without mate(pair) reads are known as singletons. I am agree with him. But 72,424 singletons in this plos one paper, make me curious to known more about singletons. Thanks, Reema,