SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
defition of singleton SNPs bongbimit Bioinformatics 0 05-22-2014 07:20 AM
Compare de-novo transcriptome assembly to genome reference guided assembly IdoBar Bioinformatics 1 04-04-2014 01:28 AM
assembly and strand definition litali Bioinformatics 1 08-31-2012 10:36 PM
Unique mapped reads definition confusing... edge Bioinformatics 6 09-10-2009 01:44 AM
FAQs & definition of terms on Assembly/MAQ etc jess Bioinformatics 2 06-03-2009 07:01 AM

Reply
 
Thread Tools
Old 09-19-2014, 02:18 AM   #1
bongbimit
Member
 
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". (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.
bongbimit is offline   Reply With Quote
Old 09-22-2014, 08:04 AM   #2
reema
Member
 
Location: Scotland

Join Date: Feb 2014
Posts: 27
Default

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,
reema 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 05:17 PM.


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