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Sampling 10X dataset when having extreme coverage

Posted By: jtran, on Dec 6, 2018 at 1:20 AM

Hi

 

I have a question regarding extreme coverage and how I can deal with it to do several assemblies with supernova.

 

We got 200X on a genome project assembly, a coverage largely higher than the recommended 56X in your guidance. I was wondering if I can subsample my dataset to get several assemblies and therefore the most infomation from it.

 

But your doc did not recommend to use --bcfrac option as it is deprecated and give worse results than using raw data. I understood that using --maxreads help to achieve a good assembly regarding the recommended 56X coverage. And I cannot use --accept-extreme-coverage because my dataset is 1,2x10^13 reads, much higher thant the supernova limit 2,14x10^9 reads.

 

Did supernova subsample different reads if I run it several times with the same --maxreads limit?

Is there a way to tell supernova to subsample different reads for the same amount of reads?

 

Joseph

 

 

 

1 Reply

Re: Sampling 10X dataset when having extreme coverage

Posted By: shauna-10x, on Dec 6, 2018 at 9:43 AM

Hi Joseph,

 

I've forwarded your email to our support team and they will be reaching out to you directly, as there may be a bit of back and forth to help answer your question.

 

Best,

Shauna