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Old 01-08-2014, 02:09 AM   #1
RyNkA
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Location: Brisbane

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Default Soap de novo trans parameters

Hi all,

I just recently trying to use SOAP denovo-trans for de novo assembly of a non-model species. I did try to run SOAP-trans but i'm kind of confuse about the options in the config file.
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3) asm_flags
This indicator decides in which part(s) the reads are used. It takes value 1(only contig assembly), 2 (only scaffold assembly), 3(both contig and scaffold assembly).
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Which to choose in my case ? I have single end reads file, with read length ranging from 30-300

Any suggestions
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Old 01-08-2014, 12:12 PM   #2
jebowers
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Without paired end reads you will only be able to construct contigs (not scaffolds). You can either specify 1 or 3.
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Old 01-08-2014, 05:56 PM   #3
RyNkA
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Quote:
Originally Posted by jebowers View Post
Without paired end reads you will only be able to construct contigs (not scaffolds). You can either specify 1 or 3.
Thanks for the answer.

That's what i was doubt about, what if i specify 3 ? What will the program behave, will it just omit scaffoldings step ?
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Old 01-09-2014, 07:45 AM   #4
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Yes the scaffolding step will happen or not, but it will only look at zero paired ends so I expect it should not take long to run.
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