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Old 09-17-2014, 03:09 AM   #1
reema
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Default What is Singletons?

Dear Friends,

I would like to ask :- What is Singletons especially in a de-novo transcriptomics assembly? I known this sound silly, but I am really very eager to known the exact information about singletons. After reading http://www.biomedcentral.com/1471-2164/14/465, I understand a bit, but not fully. I would appreciate any explaination.

Many Thanks,
Reema Singh,
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Old 09-17-2014, 12:20 PM   #2
westerman
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There are probably several different meanings for the word.

1) Before assembly reads will often be grouped into "pairs" (ones that have mates) and "singletons" (reads without a mate; generally because the potential mate is of poor quality)

2) After assembly you will have contigs formed from the merging (or assembly) of reads and then reads which can not be assembled -- these latter could be called "singletons" or "singleton contigs". The paper says "...while singletons are the remaining isolated reads..."

Personally I rarely use singleton reads when I have a large set of paired reads and almost never consider singleton contigs in the final results since they are unsupported by other reads.
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Old 09-18-2014, 02:43 AM   #3
reema
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Hi Rick,

Thanks for explaining this so clearly. It means When we align reads back to the new assembly, and in the alignment summary reads having only one pair e.g only left pair align and only right pair. Can we say these reads are singletons? Or we need to find out proper unmapped reads?

Many Thanks,
Reema Singh,
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Old 09-18-2014, 08:20 AM   #4
westerman
Rick Westerman
 
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I am not sure I understand your question.

If you align paired reads to the new assembly then one of three things can occur

1) Neither the left nor right align
2) Only one of the left or right align
3) Both the left and right align

I suppose you could call these

1) Unmapped
2) Singleton mapped
3) Paired mapped

Although that is, in my opinion, stretching the definition of what a consider a 'singleton' -- which is left read that simply doesn't have a right read and vice-versa.
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Old 09-22-2014, 07:54 AM   #5
reema
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Thanks Rick, This is really helpful

Reema Singh,
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