Confusing about definition of singleton in transcriptome assembly

[bongbimit]

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]

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,