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Old 09-19-2014, 02:18 AM   #1
Location: Ha Noi

Join Date: Dec 2013
Posts: 29
Default 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". (

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.
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Old 09-22-2014, 08:04 AM   #2
Location: Scotland

Join Date: Feb 2014
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Please see this link :- 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.

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